PADDI enrichment analysis - Reactome
Mark Ziemann
2026-04-24
Introduction
Let’s do some enrichment analysis.
suppressPackageStartupMessages({
library("gplots")
library("reshape2")
library("WGCNA")
library("dplyr")
library("DESeq2")
library("mitch")
library("MASS")
library("kableExtra")
library("ggplot2")
library("eulerr")
library("DT")
library("xlsx")
})
load("qc.Rds")Load REACTOME gene sets
reactome <- mitch::gmt_import("ReactomePathways_30oct24.gmt")Gene table
gt <- read.table("../ref/gencode.v38.genetable.tsv")
rownames(gt) <- paste(gt[,1],gt[,2])
gt[,1] <- rownames(gt)Individual contrast analysis unstratified
Start with Reactome gene sets
Firstly we do the unstratified contrasts.
- crp_t0_adj
- crp_eos_adj
- crp_pod1_adj
- dex_t0_adj
- dex_eos_adj
- dex_pod1_adj
de <- crp_t0_adj
myname <- "crp_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.m_crp_t0_adj <- mres
mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 1140 | Phosphate bond hydrolysis by NTPDase proteins | 5 | 0.0059566 | -0.7101486 | 0.0428299 |
| 1492 | SUMO is proteolytically processed | 6 | 0.0058929 | -0.6491188 | 0.0425305 |
| 1141 | Phosphate bond hydrolysis by NUDT proteins | 7 | 0.0065786 | -0.5930764 | 0.0462662 |
| 979 | NOTCH4 Activation and Transmission of Signal to the Nucleus | 10 | 0.0012734 | -0.5883349 | 0.0145002 |
| 1361 | Regulation of NFE2L2 gene expression | 8 | 0.0042832 | 0.5831694 | 0.0342860 |
| 1633 | Small interfering RNA (siRNA) biogenesis | 9 | 0.0033815 | -0.5641147 | 0.0289609 |
| 155 | Beta-oxidation of pristanoyl-CoA | 9 | 0.0045010 | -0.5467931 | 0.0352575 |
| 317 | Cytochrome c-mediated apoptotic response | 13 | 0.0006671 | -0.5450005 | 0.0088814 |
| 1186 | Processing and activation of SUMO | 10 | 0.0036639 | -0.5306130 | 0.0303707 |
| 26 | ATF6 (ATF6-alpha) activates chaperones | 12 | 0.0020613 | -0.5136563 | 0.0202662 |
| 111 | Apoptosis induced DNA fragmentation | 10 | 0.0057728 | -0.5040805 | 0.0419632 |
| 558 | Formation of apoptosome | 11 | 0.0047607 | -0.4914930 | 0.0364039 |
| 1411 | Regulation of the apoptosome activity | 11 | 0.0047607 | -0.4914930 | 0.0364039 |
| 851 | MAPK3 (ERK1) activation | 10 | 0.0073218 | -0.4897347 | 0.0496801 |
| 87 | Advanced glycosylation endproduct receptor signaling | 12 | 0.0036722 | -0.4842849 | 0.0303707 |
| 1358 | Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy | 16 | 0.0008088 | -0.4836414 | 0.0103211 |
| 454 | ER Quality Control Compartment (ERQC) | 21 | 0.0001924 | -0.4699638 | 0.0034012 |
| 104 | Antigen Presentation: Folding, assembly and peptide loading of class I MHC | 30 | 0.0000104 | -0.4649481 | 0.0003645 |
| 411 | Diseases of branched-chain amino acid catabolism | 13 | 0.0039266 | -0.4619291 | 0.0317923 |
| 989 | NRIF signals cell death from the nucleus | 15 | 0.0023779 | -0.4530801 | 0.0225726 |
| 217 | Calnexin/calreticulin cycle | 26 | 0.0000695 | -0.4506148 | 0.0015403 |
| 958 | N-glycan trimming in the ER and Calnexin/Calreticulin cycle | 35 | 0.0000052 | -0.4448310 | 0.0002191 |
| 730 | Incretin synthesis, secretion, and inactivation | 14 | 0.0045883 | -0.4375131 | 0.0355088 |
| 1692 | Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) | 14 | 0.0045883 | -0.4375131 | 0.0355088 |
| 1161 | Platelet sensitization by LDL | 16 | 0.0029621 | -0.4290576 | 0.0265489 |
| 715 | IRAK4 deficiency (TLR2/4) | 15 | 0.0050630 | -0.4179761 | 0.0381109 |
| 924 | Mitochondrial calcium ion transport | 22 | 0.0010352 | -0.4040145 | 0.0123897 |
| 1375 | Regulation of TLR by endogenous ligand | 15 | 0.0071826 | -0.4008694 | 0.0491359 |
| 661 | Golgi Associated Vesicle Biogenesis | 55 | 0.0000010 | -0.3805847 | 0.0000590 |
| 657 | Glycosphingolipid catabolism | 31 | 0.0004123 | -0.3664900 | 0.0061994 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_t0_adj_mitchreport.rds ".##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa15d77fc6.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- crp_eos_adj
myname <- "crp_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.m_crp_eos_adj <- mres
mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 550 | Formation of ATP by chemiosmotic coupling | 20 | 0.0000000 | -0.8530097 | 0.0000000 |
| 1127 | Peptide chain elongation | 88 | 0.0000000 | -0.8425531 | 0.0000000 |
| 559 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.8424613 | 0.0000000 |
| 495 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.8344500 | 0.0000000 |
| 1867 | Viral mRNA Translation | 88 | 0.0000000 | -0.8310770 | 0.0000000 |
| 815 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.8264259 | 0.0000000 |
| 946 | Modulation by Mtb of host immune system | 7 | 0.0001529 | -0.8262745 | 0.0008767 |
| 619 | GTP hydrolysis and joining of the 60S ribosomal subunit | 111 | 0.0000000 | -0.8220153 | 0.0000000 |
| 1454 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.8190467 | 0.0000000 |
| 220 | Cap-dependent Translation Initiation | 118 | 0.0000000 | -0.8166182 | 0.0000000 |
| 496 | Eukaryotic Translation Initiation | 118 | 0.0000000 | -0.8166182 | 0.0000000 |
| 572 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | -0.8125909 | 0.0000000 |
| 497 | Eukaryotic Translation Termination | 92 | 0.0000000 | -0.8098841 | 0.0000000 |
| 934 | Mitochondrial translation initiation | 90 | 0.0000000 | -0.8069804 | 0.0000000 |
| 1487 | SRP-dependent cotranslational protein targeting to membrane | 111 | 0.0000000 | -0.8054074 | 0.0000000 |
| 1514 | Selenocysteine synthesis | 92 | 0.0000000 | -0.8045771 | 0.0000000 |
| 1039 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 94 | 0.0000000 | -0.8022010 | 0.0000000 |
| 73 | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 59 | 0.0000000 | -0.7962023 | 0.0000000 |
| 933 | Mitochondrial translation elongation | 90 | 0.0000000 | -0.7937144 | 0.0000000 |
| 1803 | Translation initiation complex formation | 58 | 0.0000000 | -0.7930814 | 0.0000000 |
| 1445 | Ribosomal scanning and start codon recognition | 58 | 0.0000000 | -0.7914203 | 0.0000000 |
| 935 | Mitochondrial translation termination | 90 | 0.0000000 | -0.7834619 | 0.0000000 |
| 932 | Mitochondrial translation | 96 | 0.0000000 | -0.7762521 | 0.0000000 |
| 1433 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 100 | 0.0000000 | -0.7641189 | 0.0000000 |
| 291 | Complex III assembly | 23 | 0.0000000 | -0.7620645 | 0.0000000 |
| 1143 | Phosphate bond hydrolysis by NUDT proteins | 7 | 0.0005944 | -0.7494543 | 0.0029675 |
| 1493 | SUMO is conjugated to E1 (UBA2:SAE1) | 5 | 0.0039845 | -0.7435119 | 0.0156782 |
| 119 | Arachidonate production from DAG | 5 | 0.0040981 | -0.7412203 | 0.0160272 |
| 1802 | Translation | 293 | 0.0000000 | -0.7315688 | 0.0000000 |
| 1460 | SARS-CoV-2 modulates host translation machinery | 49 | 0.0000000 | -0.7302329 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_eos_adj_mitchreport.rds ".##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa4bbdcf4.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- crp_pod1_adj
myname <- "crp_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.m_crp_pod1_adj <- mres
mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 178 | CD163 mediating an anti-inflammatory response | 8 | 0.0000191 | 0.8726171 | 0.0003500 |
| 749 | Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 6 | 0.0005537 | 0.8140130 | 0.0062563 |
| 1430 | Response to metal ions | 6 | 0.0010264 | 0.7739132 | 0.0102691 |
| 736 | Inhibition of Signaling by Overexpressed EGFR | 5 | 0.0035418 | 0.7530497 | 0.0269992 |
| 1597 | Signaling by Overexpressed Wild-Type EGFR in Cancer | 5 | 0.0035418 | 0.7530497 | 0.0269992 |
| 569 | Formation of xylulose-5-phosphate | 5 | 0.0052750 | -0.7203690 | 0.0359019 |
| 962 | NFE2L2 regulates pentose phosphate pathway genes | 8 | 0.0005943 | 0.7010826 | 0.0065988 |
| 596 | G2/M DNA replication checkpoint | 5 | 0.0073992 | 0.6916039 | 0.0448597 |
| 554 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.6857949 | 0.0000000 |
| 1120 | Peptide chain elongation | 88 | 0.0000000 | -0.6830670 | 0.0000000 |
| 490 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.6712208 | 0.0000000 |
| 1507 | Selenocysteine synthesis | 92 | 0.0000000 | -0.6661136 | 0.0000000 |
| 1856 | Viral mRNA Translation | 88 | 0.0000000 | -0.6576144 | 0.0000000 |
| 1447 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.6564704 | 0.0000000 |
| 444 | EGFR interacts with phospholipase C-gamma | 6 | 0.0054930 | 0.6545238 | 0.0363862 |
| 492 | Eukaryotic Translation Termination | 92 | 0.0000000 | -0.6545100 | 0.0000000 |
| 567 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | -0.6435464 | 0.0000000 |
| 809 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.6423196 | 0.0000000 |
| 1909 | rRNA modification in the mitochondrion | 8 | 0.0017418 | -0.6392092 | 0.0156352 |
| 1033 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 94 | 0.0000000 | -0.6370349 | 0.0000000 |
| 1679 | Synthesis of diphthamide-EEF2 | 8 | 0.0018132 | -0.6367969 | 0.0159122 |
| 613 | GTP hydrolysis and joining of the 60S ribosomal subunit | 111 | 0.0000000 | -0.6301525 | 0.0000000 |
| 216 | Cap-dependent Translation Initiation | 118 | 0.0000000 | -0.6262678 | 0.0000000 |
| 491 | Eukaryotic Translation Initiation | 118 | 0.0000000 | -0.6262678 | 0.0000000 |
| 479 | Erythrocytes take up oxygen and release carbon dioxide | 7 | 0.0049225 | 0.6137222 | 0.0347652 |
| 72 | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 59 | 0.0000000 | -0.5977675 | 0.0000000 |
| 1793 | Translation initiation complex formation | 58 | 0.0000000 | -0.5923713 | 0.0000000 |
| 1483 | STAT5 activation downstream of FLT3 ITD mutants | 9 | 0.0021705 | 0.5901169 | 0.0181288 |
| 1356 | Regulation of NFE2L2 gene expression | 8 | 0.0038459 | 0.5901153 | 0.0287469 |
| 1426 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 100 | 0.0000000 | -0.5868312 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_pod1_adj_mitchreport.rds ".##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa5f5ffd3d.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUE## dex
de <- dex_t0_adj
myname <- "dex_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.m_dex_t0_adj <- mres
mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 1361 | Regulation of NFE2L2 gene expression | 8 | 0.0000287 | -0.8540618 | 0.0007565 |
| 856 | MECP2 regulates transcription of neuronal ligands | 5 | 0.0033550 | -0.7574022 | 0.0289911 |
| 984 | NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | 7 | 0.0005222 | -0.7570847 | 0.0075655 |
| 1148 | Phosphorylation of Emi1 | 6 | 0.0017922 | -0.7360806 | 0.0186100 |
| 969 | NFE2L2 regulating inflammation associated genes | 5 | 0.0046814 | -0.7302904 | 0.0377450 |
| 777 | Interleukin-21 signaling | 9 | 0.0002255 | -0.7099350 | 0.0042167 |
| 835 | Loss of MECP2 binding ability to the NCoR/SMRT complex | 7 | 0.0011808 | -0.7078561 | 0.0140078 |
| 1105 | POLB-Dependent Long Patch Base Excision Repair | 8 | 0.0011704 | -0.6626681 | 0.0140078 |
| 467 | Eicosanoids | 8 | 0.0018583 | 0.6353147 | 0.0190476 |
| 419 | Disorders of Developmental Biology | 12 | 0.0002037 | -0.6191631 | 0.0039261 |
| 420 | Disorders of Nervous System Development | 12 | 0.0002037 | -0.6191631 | 0.0039261 |
| 837 | Loss of function of MECP2 in Rett syndrome | 12 | 0.0002037 | -0.6191631 | 0.0039261 |
| 1130 | Pervasive developmental disorders | 12 | 0.0002037 | -0.6191631 | 0.0039261 |
| 982 | NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | 8 | 0.0034158 | -0.5976809 | 0.0292701 |
| 1837 | Type I hemidesmosome assembly | 8 | 0.0034176 | -0.5976466 | 0.0292701 |
| 987 | NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | 32 | 0.0000000 | -0.5723710 | 0.0000017 |
| 787 | Interleukin-9 signaling | 8 | 0.0060785 | -0.5601043 | 0.0455769 |
| 1192 | Processive synthesis on the C-strand of the telomere | 19 | 0.0000533 | -0.5353844 | 0.0013329 |
| 61 | Activation of PUMA and translocation to mitochondria | 9 | 0.0056593 | -0.5325821 | 0.0427986 |
| 1416 | Removal of the Flap Intermediate from the C-strand | 17 | 0.0001492 | -0.5311830 | 0.0031394 |
| 775 | Interleukin-2 signaling | 11 | 0.0024922 | -0.5265690 | 0.0234263 |
| 1845 | Unwinding of DNA | 12 | 0.0017422 | -0.5219447 | 0.0183458 |
| 986 | NR1H2 and NR1H3-mediated signaling | 38 | 0.0000000 | -0.5174032 | 0.0000024 |
| 673 | HDMs demethylate histones | 22 | 0.0000630 | -0.4926912 | 0.0014997 |
| 1486 | STAT3 nuclear events downstream of ALK signaling | 11 | 0.0047429 | -0.4917009 | 0.0377547 |
| 1724 | TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest | 18 | 0.0003072 | -0.4913001 | 0.0053111 |
| 1418 | Repression of WNT target genes | 14 | 0.0022966 | -0.4705867 | 0.0221280 |
| 676 | HDR through MMEJ (alt-NHEJ) | 12 | 0.0051789 | -0.4660612 | 0.0400793 |
| 1378 | Regulation of TP53 Activity through Acetylation | 29 | 0.0000155 | -0.4636187 | 0.0004881 |
| 1292 | RORA activates gene expression | 18 | 0.0007844 | -0.4571562 | 0.0100764 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_t0_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa4e398ac.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- dex_eos_adj
myname <- "dex_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.m_dex_eos_adj <- mres
mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 573 | Formation of the ureteric bud | 5 | 0.0014238 | 0.8236428 | 0.0338815 |
| 180 | CD163 mediating an anti-inflammatory response | 9 | 0.0000937 | 0.7518468 | 0.0035494 |
| 1208 | Protein repair | 6 | 0.0016959 | 0.7399021 | 0.0379404 |
| 369 | Defective binding of VWF variant to GPIb:IX:V | 7 | 0.0009040 | 0.7242894 | 0.0239256 |
| 476 | Enhanced binding of GP1BA variant to VWF multimer:collagen | 7 | 0.0009040 | 0.7242894 | 0.0239256 |
| 504 | FASTK family proteins regulate processing and stability of mitochondrial RNAs | 19 | 0.0000002 | 0.6869977 | 0.0000139 |
| 924 | Mitochondrial RNA degradation | 25 | 0.0000002 | 0.6015764 | 0.0000136 |
| 1814 | Translocation of ZAP-70 to Immunological synapse | 24 | 0.0000005 | -0.5944444 | 0.0000254 |
| 1419 | Replacement of protamines by nucleosomes in the male pronucleus | 13 | 0.0002912 | 0.5802644 | 0.0095353 |
| 1930 | tRNA processing in the mitochondrion | 24 | 0.0000016 | 0.5661092 | 0.0000740 |
| 182 | CD22 mediated BCR regulation | 58 | 0.0000000 | 0.5129540 | 0.0000000 |
| 1268 | RNA Polymerase I Promoter Opening | 17 | 0.0003006 | 0.5063207 | 0.0096792 |
| 1082 | PD-1 signaling | 28 | 0.0000037 | -0.5049708 | 0.0001714 |
| 263 | Chromatin modifications during the maternal to zygotic transition (MZT) | 23 | 0.0000324 | 0.5005085 | 0.0013908 |
| 1149 | Phosphorylation of CD3 and TCR zeta chains | 27 | 0.0000070 | -0.4994707 | 0.0003152 |
| 43 | Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 | 20 | 0.0002639 | 0.4711748 | 0.0087903 |
| 275 | Classical antibody-mediated complement activation | 69 | 0.0000000 | 0.4576023 | 0.0000000 |
| 1510 | Scavenging of heme from plasma | 70 | 0.0000000 | 0.4526830 | 0.0000000 |
| 1157 | Platelet Adhesion to exposed collagen | 16 | 0.0020773 | 0.4445481 | 0.0436608 |
| 1923 | rRNA processing in the mitochondrion | 24 | 0.0001795 | 0.4416989 | 0.0063045 |
| 309 | Creation of C4 and C2 activators | 71 | 0.0000000 | 0.4225994 | 0.0000001 |
| 1707 | TGFBR3 expression | 20 | 0.0013036 | -0.4152418 | 0.0318809 |
| 1243 | RHO GTPases activate PKNs | 46 | 0.0000011 | 0.4149250 | 0.0000552 |
| 1447 | Role of LAT2/NTAL/LAB on calcium mobilization | 77 | 0.0000000 | 0.4121448 | 0.0000001 |
| 100 | Amyloid fiber formation | 52 | 0.0000004 | 0.4064486 | 0.0000224 |
| 510 | FCGR activation | 76 | 0.0000000 | 0.4045583 | 0.0000002 |
| 1475 | SIRT1 negatively regulates rRNA expression | 22 | 0.0010705 | 0.4028447 | 0.0275771 |
| 1345 | Regulation of Complement cascade | 96 | 0.0000000 | 0.3889640 | 0.0000000 |
| 635 | Generation of second messenger molecules | 38 | 0.0000491 | -0.3805215 | 0.0019762 |
| 1240 | RHO GTPases activate IQGAPs | 25 | 0.0012170 | 0.3737180 | 0.0305368 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_eos_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa76043053.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- dex_pod1_adj
myname <- "dex_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.m_dex_pod1_adj <- mres
mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 67 | Activation of caspases through apoptosome-mediated cleavage | 6 | 0.0009256 | -0.7807534 | 0.0075023 |
| 1021 | Neurotransmitter clearance | 6 | 0.0019558 | 0.7300011 | 0.0136127 |
| 57 | Activation of NIMA Kinases NEK9, NEK6, NEK7 | 7 | 0.0011691 | -0.7084762 | 0.0089118 |
| 574 | Fructose metabolism | 7 | 0.0012723 | 0.7032046 | 0.0096222 |
| 484 | Establishment of Sister Chromatid Cohesion | 11 | 0.0000748 | -0.6895345 | 0.0009208 |
| 1346 | Regulation of IFNA/IFNB signaling | 12 | 0.0000463 | -0.6790484 | 0.0006304 |
| 23 | ARMS-mediated activation | 6 | 0.0041534 | -0.6756562 | 0.0256549 |
| 596 | G2/M DNA replication checkpoint | 5 | 0.0089926 | -0.6745670 | 0.0478526 |
| 774 | Interleukin-21 signaling | 9 | 0.0006451 | -0.6567083 | 0.0055079 |
| 1430 | Response to metal ions | 6 | 0.0053529 | -0.6565005 | 0.0320340 |
| 1201 | Protein repair | 6 | 0.0060969 | -0.6464913 | 0.0351716 |
| 1474 | SMAC (DIABLO) binds to IAPs | 7 | 0.0033116 | -0.6410350 | 0.0212759 |
| 1475 | SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes | 7 | 0.0033116 | -0.6410350 | 0.0212759 |
| 1476 | SMAC, XIAP-regulated apoptotic response | 7 | 0.0033116 | -0.6410350 | 0.0212759 |
| 175 | Butyrophilin (BTN) family interactions | 10 | 0.0006208 | 0.6249306 | 0.0053480 |
| 874 | Maturation of protein 3a_9683673 | 9 | 0.0014628 | -0.6124605 | 0.0107667 |
| 875 | Maturation of protein 3a_9694719 | 9 | 0.0014628 | -0.6124605 | 0.0107667 |
| 1286 | ROBO receptors bind AKAP5 | 7 | 0.0061922 | -0.5974368 | 0.0355078 |
| 782 | Interleukin-6 signaling | 10 | 0.0010825 | -0.5967801 | 0.0084535 |
| 1374 | Regulation of TP53 Activity through Association with Co-factors | 11 | 0.0006606 | 0.5929163 | 0.0056152 |
| 1831 | Type I hemidesmosome assembly | 8 | 0.0049171 | -0.5741704 | 0.0296104 |
| 1306 | RUNX3 regulates CDKN1A transcription | 7 | 0.0093040 | 0.5675959 | 0.0491016 |
| 289 | Condensation of Prometaphase Chromosomes | 11 | 0.0011605 | -0.5655862 | 0.0088832 |
| 939 | Mitotic Telophase/Cytokinesis | 13 | 0.0004214 | -0.5647834 | 0.0037828 |
| 198 | CREB1 phosphorylation through the activation of Adenylate Cyclase | 9 | 0.0040298 | -0.5535471 | 0.0252160 |
| 1058 | OAS antiviral response | 8 | 0.0080213 | -0.5412568 | 0.0439003 |
| 278 | Cohesin Loading onto Chromatin | 10 | 0.0035870 | -0.5318270 | 0.0228165 |
| 1156 | Platelet sensitization by LDL | 16 | 0.0002589 | -0.5274580 | 0.0024990 |
| 318 | Cytosolic iron-sulfur cluster assembly | 13 | 0.0013144 | 0.5145879 | 0.0098631 |
| 1357 | Regulation of NPAS4 gene expression | 11 | 0.0043096 | -0.4970256 | 0.0264498 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_pod1_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa63f6f57f.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUENow take a look at the interactions.
- m_crp_t0_adj
- m_crp_eos_adj
- m_crp_pod1_adj
- m_dex_t0_adj
- m_dex_eos_adj
- m_dex_pod1_adj
m_crp_t0_adj_up <- subset(m_crp_t0_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist>0)$set
m_crp_t0_adj_dn <- subset(m_crp_t0_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist<0)$set
m_crp_eos_adj_up <- subset(m_crp_eos_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist>0)$set
m_crp_eos_adj_dn <- subset(m_crp_eos_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist<0)$set
m_crp_pod1_adj_up <- subset(m_crp_pod1_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist>0)$set
m_crp_pod1_adj_dn <- subset(m_crp_pod1_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist<0)$set
m_dex_t0_adj_up <- subset(m_dex_t0_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist>0)$set
m_dex_t0_adj_dn <- subset(m_dex_t0_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist<0)$set
m_dex_eos_adj_up <- subset(m_dex_eos_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist>0)$set
m_dex_eos_adj_dn <- subset(m_dex_eos_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist<0)$set
m_dex_pod1_adj_up <- subset(m_dex_pod1_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist>0)$set
m_dex_pod1_adj_dn <- subset(m_dex_pod1_adj$enrichment_result,p.adjustANOVA<0.01 & s.dist<0)$set
crp_l <- list("t0 CRP up"=m_crp_t0_adj_up,"t0 CRP dn"=m_crp_t0_adj_dn,
"EOS CRP up"=m_crp_eos_adj_up, "EOS CRP dn"=m_crp_eos_adj_dn,
"POD1 CRP up"=m_crp_pod1_adj_up, "POD1 CRP dn"=m_crp_pod1_adj_dn)
plot(euler(crp_l),quantities = TRUE)## Warning in colSums(id & !empty) == 0 | merged_sets: longer object length is not
## a multiple of shorter object length
crp_l <- list("EOS CRP up"=m_crp_eos_adj_up, "EOS CRP dn"=m_crp_eos_adj_dn,
"POD1 CRP up"=m_crp_pod1_adj_up, "POD1 CRP dn"=m_crp_pod1_adj_dn)
plot(euler(crp_l),quantities = TRUE)
dex_l <- list("t0 dex up"=m_dex_t0_adj_up,"t0 dex dn"=m_dex_t0_adj_dn,
"EOS dex up"=m_dex_eos_adj_up, "EOS dex dn"=m_dex_eos_adj_dn,
"POD1 dex up"=m_dex_pod1_adj_up, "POD1 dex dn"=m_dex_pod1_adj_dn)
plot(euler(dex_l),quantities = TRUE)
dex_l <- list("EOS dex up"=m_dex_eos_adj_up, "EOS dex dn"=m_dex_eos_adj_dn,
"POD1 dex up"=m_dex_pod1_adj_up, "POD1 dex dn"=m_dex_pod1_adj_dn)
plot(euler(dex_l),quantities = TRUE)
cross_eos <- list("EOS dex up"=m_dex_eos_adj_up, "EOS dex dn"=m_dex_eos_adj_dn,
"EOS CRP up"=m_crp_eos_adj_up, "EOS CRP dn"=m_crp_eos_adj_dn)
plot(euler(cross_eos),quantities = TRUE)
cross_pod1 <- list("POD1 dex up"=m_dex_pod1_adj_up, "POD1 dex dn"=m_dex_pod1_adj_dn,
"POD1 CRP up"=m_crp_pod1_adj_up, "POD1 CRP dn"=m_crp_pod1_adj_dn)
plot(euler(cross_pod1),quantities = TRUE)
intersect(m_crp_pod1_adj_up, m_dex_pod1_adj_dn)## [1] "Interaction between L1 and Ankyrins"
## [2] "Formation of the beta-catenin:TCF transactivating complex"
## [3] "Antimicrobial peptides"
## [4] "Transcriptional regulation of granulopoiesis"
## [5] "HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand"
## [6] "Factors involved in megakaryocyte development and platelet production"
## [7] "Platelet homeostasis"
## [8] "Anti-inflammatory response favouring Leishmania parasite infection"
## [9] "Leishmania parasite growth and survival"
## [10] "Nuclear events mediated by NFE2L2"
## [11] "VEGFA-VEGFR2 Pathway"
## [12] "Antigen activates B Cell Receptor (BCR) leading to generation of second messengers"
## [13] "Regulation of actin dynamics for phagocytic cup formation"
## [14] "Binding and Uptake of Ligands by Scavenger Receptors"
## [15] "COPI-dependent Golgi-to-ER retrograde traffic"
## [16] "Golgi-to-ER retrograde transport"
## [17] "Neutrophil degranulation"
## [18] "FCGR3A-mediated phagocytosis"
## [19] "Leishmania phagocytosis"
## [20] "Parasite infection"
## [21] "Role of LAT2/NTAL/LAB on calcium mobilization"
## [22] "Fcgamma receptor (FCGR) dependent phagocytosis"
## [23] "Muscle contraction"
## [24] "FCERI mediated Ca+2 mobilization"
## [25] "Leishmania infection"
## [26] "Parasitic Infection Pathways"
## [27] "Hemostasis"
## [28] "Signaling by VEGF"
## [29] "FCGR3A-mediated IL10 synthesis"
## [30] "Signaling by ALK fusions and activated point mutants"
## [31] "Signaling by ALK in cancer"
## [32] "FCERI mediated MAPK activation"
## [33] "Response to elevated platelet cytosolic Ca2+"
## [34] "Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes"
## [35] "Epigenetic regulation of gene expression by MLL3 and MLL4 complexes"
## [36] "MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis"
## [37] "Cell surface interactions at the vascular wall"
## [38] "Signaling by Interleukins"
## [39] "Platelet degranulation"
## [40] "Platelet activation, signaling and aggregation"
## [41] "KEAP1-NFE2L2 pathway"
## [42] "Transport to the Golgi and subsequent modification"
## [43] "Transcriptional regulation by RUNX1"
## [44] "ER to Golgi Anterograde Transport"
## [45] "RHO GTPase Effectors"
## [46] "ESR-mediated signaling"
## [47] "TCF dependent signaling in response to WNT"
## [48] "Fc epsilon receptor (FCERI) signaling"
## [49] "Signaling by the B Cell Receptor (BCR)"
## [50] "MAPK family signaling cascades"
## [51] "Vesicle-mediated transport"
## [52] "Signaling by Rho GTPases"
## [53] "Signaling by Rho GTPases, Miro GTPases and RHOBTB3"
## [54] "MAPK1/MAPK3 signaling"
## [55] "RHO GTPase cycle"
## [56] "RAF/MAP kinase cascade"
## [57] "Signaling by WNT"
## [58] "Cellular response to chemical stress"
## [59] "Membrane Trafficking"
## [60] "Signal Transduction"
## [61] "Innate Immune System"
## [62] "Intra-Golgi and retrograde Golgi-to-ER traffic"
## [63] "Diseases of signal transduction by growth factor receptors and second messengers"
## [64] "Immune System"
## [65] "Cytokine Signaling in Immune system"intersect(m_crp_pod1_adj_dn, m_dex_pod1_adj_up)## [1] "Formation of a pool of free 40S subunits"
## [2] "Peptide chain elongation"
## [3] "Eukaryotic Translation Elongation"
## [4] "Selenocysteine synthesis"
## [5] "Viral mRNA Translation"
## [6] "Eukaryotic Translation Termination"
## [7] "L13a-mediated translational silencing of Ceruloplasmin expression"
## [8] "Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)"
## [9] "GTP hydrolysis and joining of the 60S ribosomal subunit"
## [10] "Cap-dependent Translation Initiation"
## [11] "Eukaryotic Translation Initiation"
## [12] "Response of EIF2AK4 (GCN2) to amino acid deficiency"
## [13] "Selenoamino acid metabolism"
## [14] "Major pathway of rRNA processing in the nucleolus and cytosol"
## [15] "rRNA processing in the nucleus and cytosol"
## [16] "Influenza Viral RNA Transcription and Replication"
## [17] "rRNA processing"
## [18] "Influenza Infection"Multi-contrast enrichment analysis.
l1 <- list("crp_t0_adj"=crp_t0_adj,"crp_eos_adj"=crp_eos_adj,
"crp_pod1_adj"=crp_pod1_adj,"dex_t0_adj"=dex_t0_adj,
"dex_eos_adj"=dex_eos_adj,"dex_pod1_adj"=dex_pod1_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21771.6666666667## Note: no. genes in output = 21032## Note: estimated proportion of input genes in output = 0.966mm1 <- mitch_calc(x=m1,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:9)]
rownames(top) <- top[,1]
top[,1] = NULL
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(6,25), cexRow=0.6, cexCol=0.8 )
as.matrix(top) |> kbl(caption="Top REACTOMEs in multi enrichment analysis") |> kable_paper("hover", full_width = F)| s.crp_t0_adj | s.crp_eos_adj | s.crp_pod1_adj | s.dex_t0_adj | s.dex_eos_adj | s.dex_pod1_adj | |
|---|---|---|---|---|---|---|
| Regulation of NFE2L2 gene expression | 0.5891243 | 0.6426703 | 0.5937738 | -0.8527635 | -0.1618626 | 0.0422256 |
| Protein repair | -0.5129839 | -0.4712578 | 0.3864580 | 0.4543422 | 0.7444117 | -0.6464060 |
| G2/M DNA replication checkpoint | -0.1564940 | -0.5453084 | 0.6956294 | -0.4163314 | 0.6024920 | -0.6742854 |
| Interleukin-21 signaling | 0.2427553 | 0.6305634 | 0.3235980 | -0.7074844 | -0.5108743 | -0.6565983 |
| Response to metal ions | 0.2238815 | -0.4391388 | 0.7772440 | -0.1266210 | 0.5004439 | -0.6564412 |
| Formation of xylulose-5-phosphate | -0.5646169 | -0.5993342 | -0.7188187 | -0.0256908 | -0.5512817 | 0.2090550 |
| MECP2 regulates transcription of neuronal ligands | 0.2891616 | 0.4716507 | -0.1094307 | -0.7554953 | -0.7264660 | -0.2341085 |
| CD163 mediating an anti-inflammatory response | -0.1675466 | 0.0306198 | 0.8753092 | 0.0381707 | 0.7841990 | 0.0577911 |
| Defective binding of VWF variant to GPIb:IX:V | 0.4129453 | -0.7073667 | 0.3276835 | 0.2818757 | 0.7251153 | -0.1213583 |
| Enhanced binding of GP1BA variant to VWF multimer:collagen | 0.4129453 | -0.7073667 | 0.3276835 | 0.2818757 | 0.7251153 | -0.1213583 |
| SUMO is conjugated to E1 (UBA2:SAE1) | -0.6691111 | -0.7382794 | -0.2370952 | 0.0035098 | 0.3656727 | -0.4095211 |
| Formation of a pool of free 40S subunits | -0.2566384 | -0.8482740 | -0.6834190 | 0.1132391 | 0.0326183 | 0.2670024 |
| Peptide chain elongation | -0.2300788 | -0.8496303 | -0.6805657 | 0.1099118 | 0.0032384 | 0.2732460 |
| Eukaryotic Translation Elongation | -0.2150471 | -0.8408237 | -0.6685987 | 0.1031685 | -0.0006613 | 0.2638263 |
| Tandem pore domain potassium channels | -0.2743045 | 0.4669710 | 0.3646455 | -0.4240928 | -0.6839112 | -0.4323679 |
| Viral mRNA Translation | -0.2357093 | -0.8380367 | -0.6547938 | 0.1134164 | 0.0177537 | 0.2422804 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.2894357 | -0.8311029 | -0.6395161 | 0.1317048 | 0.0702405 | 0.2271093 |
| MET activates PI3K/AKT signaling | -0.4461597 | 0.5910020 | 0.4899700 | 0.2375137 | 0.4361725 | -0.4579160 |
| Type I hemidesmosome assembly | 0.1838613 | 0.3568065 | 0.5685883 | -0.5945110 | -0.2748288 | -0.5740939 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.2881569 | -0.8265132 | -0.6271902 | 0.1368060 | 0.0694328 | 0.2223436 |
| Modulation by Mtb of host immune system | -0.4328928 | -0.8225786 | -0.3276711 | 0.1432920 | 0.4856463 | -0.0329472 |
| Selenocysteine synthesis | -0.2285379 | -0.8105845 | -0.6634018 | 0.0895478 | -0.0035206 | 0.2575803 |
| SARS-CoV-1 modulates host translation machinery | -0.1977811 | -0.8159914 | -0.6547094 | 0.1223699 | 0.0174901 | 0.2659845 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.2805442 | -0.8092074 | -0.6417244 | 0.1415314 | 0.0843499 | 0.2150078 |
| Cap-dependent Translation Initiation | -0.2791662 | -0.8205328 | -0.6233219 | 0.1298291 | 0.0611384 | 0.2299887 |
| Eukaryotic Translation Initiation | -0.2791662 | -0.8205328 | -0.6233219 | 0.1298291 | 0.0611384 | 0.2299887 |
| Phosphate bond hydrolysis by NUDT proteins | -0.5898896 | -0.7452421 | -0.4329744 | 0.2570749 | 0.2305894 | 0.0152675 |
| Eukaryotic Translation Termination | -0.2201428 | -0.8159875 | -0.6516199 | 0.0855239 | 0.0029665 | 0.2416297 |
| POLB-Dependent Long Patch Base Excision Repair | 0.1600195 | -0.2593584 | -0.5704790 | -0.6590682 | -0.5523687 | 0.1608162 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.2287859 | -0.8079049 | -0.6339670 | 0.0859748 | 0.0370297 | 0.2443878 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.3254717 | -0.7927068 | -0.5959163 | 0.1553175 | 0.1335236 | 0.2064196 |
| Translation initiation complex formation | -0.3192935 | -0.7895309 | -0.5904996 | 0.1471165 | 0.1325533 | 0.1938952 |
| Ribosomal scanning and start codon recognition | -0.3196421 | -0.7878260 | -0.5767469 | 0.1538374 | 0.1338340 | 0.1999619 |
| Fructose metabolism | -0.2746866 | -0.2257924 | -0.5791812 | 0.1400170 | -0.3878988 | 0.7030882 |
| SRP-dependent cotranslational protein targeting to membrane | -0.3137176 | -0.8098174 | -0.5609285 | 0.0984688 | 0.1043399 | 0.0969558 |
| RUNX1 regulates transcription of genes involved in BCR signaling | 0.0000793 | 0.3428929 | 0.5935667 | 0.1495767 | 0.6900346 | -0.3422429 |
| Replacement of protamines by nucleosomes in the male pronucleus | -0.2815335 | -0.6127894 | 0.2507850 | 0.2857120 | 0.6285284 | -0.3005788 |
| Activation of caspases through apoptosome-mediated cleavage | -0.5968325 | -0.2860427 | 0.1480389 | 0.0998763 | -0.0273947 | -0.7806684 |
| Phosphorylation of Emi1 | 0.2315229 | -0.2473129 | 0.4386315 | -0.7339167 | 0.0985764 | -0.4531057 |
| FASTK family proteins regulate processing and stability of mitochondrial RNAs | -0.0944954 | -0.7225026 | -0.0366565 | 0.1400261 | 0.6907979 | 0.1462929 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.2305214 | -0.7689820 | -0.5831887 | 0.1372957 | 0.0329367 | 0.2135177 |
| Post-transcriptional silencing by small RNAs | -0.2110888 | 0.7144488 | 0.3228877 | -0.2452251 | -0.3767420 | -0.4195753 |
| CD22 mediated BCR regulation | 0.1548769 | -0.5511666 | 0.2320549 | -0.4066838 | 0.5203965 | -0.4517416 |
| Mitochondrial translation initiation | -0.1122264 | -0.8032725 | -0.5660703 | -0.0899850 | 0.1013678 | 0.0875858 |
| Regulation of NPAS4 gene expression | -0.1496123 | 0.6113497 | 0.2834784 | -0.3270452 | -0.4092315 | -0.4968062 |
| SUMO is transferred from E1 to E2 (UBE2I, UBC9) | -0.4931748 | -0.6900696 | -0.3916222 | -0.0716358 | 0.2195957 | -0.2664243 |
| Formation of ATP by chemiosmotic coupling | -0.3101656 | -0.8499857 | -0.2985342 | -0.0291072 | 0.2920141 | -0.0351323 |
| Mitochondrial translation elongation | -0.1010261 | -0.7899925 | -0.5572088 | -0.0970129 | 0.1003247 | 0.1107514 |
| Activation of NIMA Kinases NEK9, NEK6, NEK7 | 0.0210973 | -0.0371734 | 0.4603975 | -0.4826159 | 0.1372584 | -0.7083880 |
| NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose | -0.0419175 | 0.1356637 | -0.0841109 | -0.6943359 | -0.4581823 | 0.4916060 |
mitch_report(res=mm1,outfile="multireactome_all_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/multireactome_all_mitchreport.rds ".##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa5e86b7b2.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEThis might work better if we work on each timepoint separately.
l1 <- list("crp_t0_adj"=crp_t0_adj, "dex_t0_adj"=dex_t0_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mm1 <- mitch_calc(x=m1,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:5)]
rownames(top) <- top[,1]
top[,1] = NULL
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none", margins = c(6,25), cexRow=0.6, cexCol=0.8 )
as.matrix(top) |> kbl(caption="Top REACTOMEs in multi enrichment analysis at t0") |> kable_paper("hover", full_width = F)| s.crp_t0_adj | s.dex_t0_adj | |
|---|---|---|
| Regulation of NFE2L2 gene expression | 0.5831694 | -0.8540618 |
| MECP2 regulates transcription of neuronal ligands | 0.2836222 | -0.7574022 |
| Phosphorylation of Emi1 | 0.2254696 | -0.7360806 |
| NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | -0.0547631 | -0.7570847 |
| Interleukin-21 signaling | 0.2372312 | -0.7099350 |
| Loss of MECP2 binding ability to the NCoR/SMRT complex | 0.1218432 | -0.7078561 |
| Phosphate bond hydrolysis by NTPDase proteins | -0.7101486 | -0.0293711 |
| NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose | -0.0498422 | -0.6972879 |
| POLB-Dependent Long Patch Base Excision Repair | 0.1545833 | -0.6626681 |
| SUMO is proteolytically processed | -0.6491188 | -0.0691395 |
| Disorders of Developmental Biology | 0.1587519 | -0.6191631 |
| Disorders of Nervous System Development | 0.1587519 | -0.6191631 |
| Loss of function of MECP2 in Rett syndrome | 0.1587519 | -0.6191631 |
| Pervasive developmental disorders | 0.1587519 | -0.6191631 |
| Eicosanoids | 0.0688180 | 0.6353147 |
| Unwinding of DNA | 0.3670433 | -0.5219447 |
| Type I hemidesmosome assembly | 0.1770309 | -0.5976466 |
| NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | -0.1419586 | -0.5976809 |
| Repression of WNT target genes | 0.3720064 | -0.4705867 |
| NOTCH4 Activation and Transmission of Signal to the Nucleus | -0.5883349 | 0.0466972 |
| Small interfering RNA (siRNA) biogenesis | -0.5641147 | 0.1233907 |
| NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | -0.0718215 | -0.5723710 |
| Interleukin-2 signaling | 0.2021842 | -0.5265690 |
| Beta-oxidation of pristanoyl-CoA | -0.5467931 | 0.1305165 |
| TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest | 0.2701965 | -0.4913001 |
| Cytochrome c-mediated apoptotic response | -0.5450005 | 0.1278203 |
| Formation of annular gap junctions | -0.3688564 | -0.4207228 |
| Synthesis of pyrophosphates in the cytosol | -0.4556536 | -0.2980857 |
| Processing and activation of SUMO | -0.5306130 | -0.1210156 |
| Processive synthesis on the C-strand of the telomere | 0.0634320 | -0.5353844 |
| TGFBR3 regulates TGF-beta signaling | -0.2281241 | -0.4854771 |
| Glycosphingolipid transport | -0.4072961 | -0.3440843 |
| Removal of the Flap Intermediate from the C-strand | -0.0132732 | -0.5311830 |
| Cohesin Loading onto Chromatin | -0.4495151 | -0.2809515 |
| NR1H2 and NR1H3-mediated signaling | -0.1034382 | -0.5174032 |
| ATF6 (ATF6-alpha) activates chaperones | -0.5136563 | -0.0869094 |
| Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy | -0.4836414 | 0.1770900 |
| Miscellaneous substrates | 0.4991309 | 0.1048280 |
| SARS-CoV-2 modulates autophagy | -0.3592571 | -0.3609456 |
| Antigen Presentation: Folding, assembly and peptide loading of class I MHC | -0.4649481 | -0.2040965 |
| Response of EIF2AK1 (HRI) to heme deficiency | -0.2431696 | 0.4425787 |
| Advanced glycosylation endproduct receptor signaling | -0.4842849 | 0.1357093 |
| HDMs demethylate histones | 0.0890637 | -0.4926912 |
| MAPK3 (ERK1) activation | -0.4897347 | -0.0997987 |
| TGFBR3 PTM regulation | -0.4738792 | -0.1511528 |
| Fatty acids | 0.3749085 | 0.3264569 |
| MASTL Facilitates Mitotic Progression | -0.4835590 | -0.0666789 |
| ATF6 (ATF6-alpha) activates chaperone genes | -0.4699085 | -0.1211894 |
| Establishment of Sister Chromatid Cohesion | -0.4163669 | -0.2387242 |
| HSF1-dependent transactivation | 0.2537546 | -0.4033974 |
mitch_report(res=mm1,outfile="multireactome_t0_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/multireactome_t0_mitchreport.rds ".##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa458dfeb1.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEl1 <- list("crp_eos_adj"=crp_eos_adj, "dex_eos_adj"=dex_eos_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mm1 <- mitch_calc(x=m1,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:5)]
rownames(top) <- top[,1]
top[,1] = NULL
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none", margins = c(6,25), cexRow=0.6, cexCol=0.8 )
as.matrix(top) |> kbl(caption="Top REACTOMEs in multi enrichment analysis at EOS") |> kable_paper("hover", full_width = F)| s.crp_eos_adj | s.dex_eos_adj | |
|---|---|---|
| FASTK family proteins regulate processing and stability of mitochondrial RNAs | -0.7269863 | 0.6869977 |
| Formation of the ureteric bud | -0.4916795 | 0.8236428 |
| Modulation by Mtb of host immune system | -0.8262745 | 0.4784077 |
| Mitochondrial RNA degradation | -0.6840266 | 0.6015764 |
| Defective binding of VWF variant to GPIb:IX:V | -0.5438731 | 0.7242894 |
| Enhanced binding of GP1BA variant to VWF multimer:collagen | -0.5438731 | 0.7242894 |
| Formation of ATP by chemiosmotic coupling | -0.8530097 | 0.2819965 |
| Protein repair | -0.4770760 | 0.7399021 |
| MECP2 regulates transcription of neuronal ligands | 0.4676003 | -0.7329635 |
| tRNA processing in the mitochondrion | -0.6357035 | 0.5661092 |
| RNA Polymerase I Promoter Opening | -0.6758712 | 0.5063207 |
| Peptide chain elongation | -0.8425531 | -0.0139770 |
| Formation of a pool of free 40S subunits | -0.8424613 | 0.0159642 |
| Eukaryotic Translation Elongation | -0.8344500 | -0.0176041 |
| Viral mRNA Translation | -0.8310770 | 0.0005155 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.8264259 | 0.0539798 |
| SUMO is conjugated to E1 (UBA2:SAE1) | -0.7435119 | 0.3562608 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.8220153 | 0.0532202 |
| Formation of xylulose-5-phosphate | -0.6024007 | -0.5603892 |
| SARS-CoV-1 modulates host translation machinery | -0.8190467 | 0.0051728 |
| Cap-dependent Translation Initiation | -0.8166182 | 0.0453687 |
| Eukaryotic Translation Initiation | -0.8166182 | 0.0453687 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.8125909 | 0.0726852 |
| Interleukin-21 signaling | 0.6277601 | -0.5174271 |
| Mitochondrial translation initiation | -0.8069804 | 0.0908931 |
| rRNA processing in the mitochondrion | -0.6804399 | 0.4416989 |
| SRP-dependent cotranslational protein targeting to membrane | -0.8054074 | 0.0881037 |
| Eukaryotic Translation Termination | -0.8098841 | -0.0138044 |
| Post-transcriptional silencing by small RNAs | 0.7119602 | -0.3856857 |
| Packaging Of Telomere Ends | -0.6982394 | 0.4097883 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.7962023 | 0.1223012 |
| Selenocysteine synthesis | -0.8045771 | -0.0205017 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.8022010 | 0.0201839 |
| Translation initiation complex formation | -0.7930814 | 0.1213301 |
| Ribosomal scanning and start codon recognition | -0.7914203 | 0.1226345 |
| Mitochondrial translation elongation | -0.7937144 | 0.0899113 |
| Mitochondrial translation termination | -0.7834619 | 0.0900208 |
| Phosphate bond hydrolysis by NUDT proteins | -0.7494543 | 0.2234319 |
| Mitochondrial translation | -0.7762521 | 0.0838565 |
| Regulation of CDH11 mRNA translation by microRNAs | 0.6300191 | -0.4579828 |
| Regulation of NPAS4 mRNA translation | 0.6300191 | -0.4579828 |
| Replacement of protamines by nucleosomes in the male pronucleus | -0.5182949 | 0.5802644 |
| Complex III assembly | -0.7620645 | 0.0632627 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.7641189 | 0.0164829 |
| RUNX1 regulates transcription of genes involved in BCR signaling | 0.3380166 | 0.6845966 |
| Arachidonate production from DAG | -0.7412203 | 0.1408020 |
| CD163 mediating an anti-inflammatory response | 0.0320247 | 0.7518468 |
| Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 | -0.5815119 | 0.4711748 |
| CD22 mediated BCR regulation | -0.5349692 | 0.5129540 |
| Regulation of NPAS4 gene expression | 0.6083070 | -0.4176410 |
mitch_report(res=mm1,outfile="multireactome_eos_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/multireactome_eos_mitchreport.rds ".##
##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa170b4f36.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEl1 <- list("crp_pod1_adj"=crp_pod1_adj, "dex_pod1_adj"=dex_pod1_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mm1 <- mitch_calc(x=m1,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:5)]
rownames(top) <- top[,1]
top[,1] = NULL
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none", margins = c(6,25), cexRow=0.6, cexCol=0.8 )
as.matrix(top) |> kbl(caption="Top REACTOMEs in multi enrichment analysis at POD1") |> kable_paper("hover", full_width = F)| s.crp_pod1_adj | s.dex_pod1_adj | |
|---|---|---|
| Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 0.8140130 | -0.6102195 |
| Response to metal ions | 0.7739132 | -0.6565005 |
| G2/M DNA replication checkpoint | 0.6916039 | -0.6745670 |
| Fructose metabolism | -0.5808825 | 0.7032046 |
| CD163 mediating an anti-inflammatory response | 0.8726171 | 0.0578724 |
| Butyrophilin (BTN) family interactions | -0.5751165 | 0.6249306 |
| Activation of NIMA Kinases NEK9, NEK6, NEK7 | 0.4563548 | -0.7084762 |
| Regulation of IFNA/IFNB signaling | 0.4407278 | -0.6790484 |
| Type I hemidesmosome assembly | 0.5655331 | -0.5741704 |
| Activation of caspases through apoptosome-mediated cleavage | 0.1436752 | -0.7807534 |
| Inhibition of Signaling by Overexpressed EGFR | 0.7530497 | 0.2023532 |
| Signaling by Overexpressed Wild-Type EGFR in Cancer | 0.7530497 | 0.2023532 |
| Establishment of Sister Chromatid Cohesion | 0.3437444 | -0.6895345 |
| Maturation of protein 3a_9683673 | 0.4537229 | -0.6124605 |
| Maturation of protein 3a_9694719 | 0.4537229 | -0.6124605 |
| Neurotransmitter clearance | -0.1916349 | 0.7300011 |
| Synthesis of diphthamide-EEF2 | -0.6367969 | 0.3932572 |
| NFE2L2 regulates pentose phosphate pathway genes | 0.7010826 | -0.2182984 |
| Formation of a pool of free 40S subunits | -0.6857949 | 0.2577601 |
| Peptide chain elongation | -0.6830670 | 0.2626785 |
| Interleukin-21 signaling | 0.3206029 | -0.6567083 |
| Mitotic Telophase/Cytokinesis | 0.4479429 | -0.5647834 |
| Eukaryotic Translation Elongation | -0.6712208 | 0.2539220 |
| Selenocysteine synthesis | -0.6661136 | 0.2476438 |
| SARS-CoV-1 modulates host translation machinery | -0.6564704 | 0.2660183 |
| Viral mRNA Translation | -0.6576144 | 0.2320566 |
| Eukaryotic Translation Termination | -0.6545100 | 0.2318591 |
| EGFR interacts with phospholipase C-gamma | 0.6545238 | 0.2238434 |
| Platelet sensitization by LDL | 0.4364847 | -0.5274580 |
| Interleukin-6 signaling | 0.3321000 | -0.5967801 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.6370349 | 0.2347917 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.6423196 | 0.2190624 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.6435464 | 0.2150297 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.6301525 | 0.2144120 |
| Cap-dependent Translation Initiation | -0.6262678 | 0.2224529 |
| Eukaryotic Translation Initiation | -0.6262678 | 0.2224529 |
| Cohesin Loading onto Chromatin | 0.3900202 | -0.5318270 |
| N-Glycan antennae elongation | 0.4727885 | -0.4595672 |
| SMAC (DIABLO) binds to IAPs | 0.0041151 | -0.6410350 |
| SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes | 0.0041151 | -0.6410350 |
| SMAC, XIAP-regulated apoptotic response | 0.0041151 | -0.6410350 |
| Common Pathway of Fibrin Clot Formation | 0.4487687 | -0.4556280 |
| rRNA modification in the mitochondrion | -0.6392092 | -0.0022594 |
| Regulation of TP53 Activity through Association with Co-factors | -0.2347836 | 0.5929163 |
| Condensation of Prometaphase Chromosomes | 0.2865849 | -0.5655862 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.5977675 | 0.2064351 |
| Translation initiation complex formation | -0.5923713 | 0.1939137 |
| Regulation of IFNG signaling | 0.3808694 | -0.4926584 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.5868312 | 0.2047955 |
| Interaction between L1 and Ankyrins | 0.4903443 | -0.3804806 |
mitch_report(res=mm1,outfile="multireactome_pod1_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpsiUaL8/multireactome_pod1_mitchreport.rds ".##
##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa681e1b61.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEIndividual contrast analysis stratified
- crp_t0_a_adj
- crp_t0_b_adj
- crp_eos_a_adj
- crp_eos_b_adj
- crp_pod1_a_adj
- crp_pod1_b_adj
- dex_crplo_t0_adj
- dex_crphi_t0_adj
- dex_crplo_eos_adj
- dex_crphi_eos_adj
- dex_crplo_pod1_adj
- dex_crphi_pod1_adj
de <- crp_t0_a_adj
myname <- "crp_t0_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 943 | Modulation by Mtb of host immune system | 7 | 0.0001741 | -0.8192118 | 0.0009451 |
| 1125 | Peptide chain elongation | 87 | 0.0000000 | -0.8159421 | 0.0000000 |
| 879 | Maturation of spike protein_9683686 | 5 | 0.0017668 | -0.8074000 | 0.0071527 |
| 1862 | Viral mRNA Translation | 87 | 0.0000000 | -0.8061612 | 0.0000000 |
| 547 | Formation of ATP by chemiosmotic coupling | 20 | 0.0000000 | -0.7990618 | 0.0000000 |
| 492 | Eukaryotic Translation Elongation | 92 | 0.0000000 | -0.7971158 | 0.0000000 |
| 556 | Formation of a pool of free 40S subunits | 99 | 0.0000000 | -0.7868520 | 0.0000000 |
| 1452 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.7859506 | 0.0000000 |
| 494 | Eukaryotic Translation Termination | 91 | 0.0000000 | -0.7823198 | 0.0000000 |
| 659 | Glycosphingolipid transport | 7 | 0.0004069 | -0.7715776 | 0.0020368 |
| 1512 | Selenocysteine synthesis | 91 | 0.0000000 | -0.7670303 | 0.0000000 |
| 1037 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 93 | 0.0000000 | -0.7653537 | 0.0000000 |
| 1647 | Sulfide oxidation to sulfate | 5 | 0.0032852 | -0.7590853 | 0.0120812 |
| 1485 | SRP-dependent cotranslational protein targeting to membrane | 110 | 0.0000000 | -0.7565032 | 0.0000000 |
| 812 | L13a-mediated translational silencing of Ceruloplasmin expression | 109 | 0.0000000 | -0.7511447 | 0.0000000 |
| 557 | Formation of annular gap junctions | 10 | 0.0000428 | -0.7470997 | 0.0002571 |
| 616 | GTP hydrolysis and joining of the 60S ribosomal subunit | 110 | 0.0000000 | -0.7368499 | 0.0000000 |
| 150 | Beta oxidation of hexanoyl-CoA to butanoyl-CoA | 5 | 0.0048307 | -0.7276927 | 0.0163310 |
| 1141 | Phosphate bond hydrolysis by NUDT proteins | 7 | 0.0009235 | -0.7229893 | 0.0040817 |
| 218 | Cap-dependent Translation Initiation | 117 | 0.0000000 | -0.7219898 | 0.0000000 |
| 493 | Eukaryotic Translation Initiation | 117 | 0.0000000 | -0.7219898 | 0.0000000 |
| 1431 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 99 | 0.0000000 | -0.7211822 | 0.0000000 |
| 569 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | -0.7012246 | 0.0000000 |
| 72 | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 59 | 0.0000000 | -0.6828999 | 0.0000000 |
| 1799 | Translation initiation complex formation | 58 | 0.0000000 | -0.6788402 | 0.0000000 |
| 1443 | Ribosomal scanning and start codon recognition | 58 | 0.0000000 | -0.6711554 | 0.0000000 |
| 1491 | SUMO is conjugated to E1 (UBA2:SAE1) | 5 | 0.0095891 | -0.6688772 | 0.0286040 |
| 577 | Fructose metabolism | 7 | 0.0022287 | -0.6673702 | 0.0088005 |
| 1511 | Selenoamino acid metabolism | 114 | 0.0000000 | -0.6654571 | 0.0000000 |
| 1185 | Prevention of phagosomal-lysosomal fusion | 9 | 0.0005886 | -0.6614976 | 0.0027801 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_t0_a_adj_mitchreport.rds ".##
##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa5d2a6aa7.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- crp_t0_b_adj
myname <- "crp_t0_b_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 487 | Establishment of Sister Chromatid Cohesion | 11 | 0.0000674 | -0.6938394 | 0.0108226 |
| 280 | Cohesin Loading onto Chromatin | 10 | 0.0002114 | -0.6765142 | 0.0271628 |
| 1675 | Synthesis of PIPs at the late endosome membrane | 11 | 0.0003485 | -0.6226559 | 0.0317967 |
| 1674 | Synthesis of PIPs at the early endosome membrane | 16 | 0.0000300 | -0.6025613 | 0.0082676 |
| 1625 | Signaling by cytosolic FGFR1 fusion mutants | 18 | 0.0006981 | -0.4615189 | 0.0343915 |
| 724 | Impaired BRCA2 binding to PALB2 | 24 | 0.0002600 | -0.4306128 | 0.0294706 |
| 511 | FGFR1 mutant receptor activation | 25 | 0.0007139 | -0.3909673 | 0.0343915 |
| 359 | Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function | 25 | 0.0008235 | -0.3864152 | 0.0344970 |
| 360 | Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function | 25 | 0.0008235 | -0.3864152 | 0.0344970 |
| 369 | Defective homologous recombination repair (HRR) due to BRCA1 loss of function | 25 | 0.0008235 | -0.3864152 | 0.0344970 |
| 371 | Defective homologous recombination repair (HRR) due to PALB2 loss of function | 25 | 0.0008235 | -0.3864152 | 0.0344970 |
| 1560 | Signaling by FGFR1 in disease | 32 | 0.0001903 | -0.3810960 | 0.0271628 |
| 1818 | Transport of Ribonucleoproteins into the Host Nucleus | 32 | 0.0013715 | -0.3268786 | 0.0489408 |
| 725 | Impaired BRCA2 binding to RAD51 | 35 | 0.0011143 | -0.3183735 | 0.0421029 |
| 1184 | Presynaptic phase of homologous DNA pairing and strand exchange | 40 | 0.0005813 | -0.3143083 | 0.0343915 |
| 180 | CD22 mediated BCR regulation | 59 | 0.0000360 | 0.3109448 | 0.0082676 |
| 370 | Defective homologous recombination repair (HRR) due to BRCA2 loss of function | 41 | 0.0006269 | -0.3086083 | 0.0343915 |
| 407 | Diseases of DNA Double-Strand Break Repair | 41 | 0.0006269 | -0.3086083 | 0.0343915 |
| 990 | NS1 Mediated Effects on Host Pathways | 40 | 0.0007562 | -0.3077462 | 0.0344970 |
| 1676 | Synthesis of PIPs at the plasma membrane | 52 | 0.0002069 | -0.2973921 | 0.0271628 |
| 700 | Homologous DNA Pairing and Strand Exchange | 43 | 0.0007505 | -0.2970196 | 0.0344970 |
| 720 | ISG15 antiviral mechanism | 72 | 0.0000229 | -0.2885548 | 0.0082676 |
| 1508 | Scavenging of heme from plasma | 71 | 0.0000482 | 0.2789035 | 0.0084366 |
| 661 | Golgi Associated Vesicle Biogenesis | 55 | 0.0004046 | -0.2756810 | 0.0324897 |
| 408 | Diseases of DNA repair | 51 | 0.0013378 | -0.2596181 | 0.0486402 |
| 273 | Classical antibody-mediated complement activation | 70 | 0.0004777 | 0.2414050 | 0.0343915 |
| 742 | Initial triggering of complement | 80 | 0.0002474 | 0.2369791 | 0.0294706 |
| 307 | Creation of C4 and C2 activators | 72 | 0.0006785 | 0.2315783 | 0.0343915 |
| 598 | G2/M DNA damage checkpoint | 66 | 0.0012627 | -0.2294755 | 0.0467919 |
| 1381 | Regulation of TP53 Activity through Phosphorylation | 88 | 0.0003953 | -0.2184915 | 0.0324897 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_t0_b_adj_mitchreport.rds ".##
##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa19264ee1.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- crp_eos_a_adj
myname <- "crp_eos_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 119 | Arachidonate production from DAG | 5 | 0.0015494 | -0.8173138 | 0.0107679 |
| 550 | Formation of ATP by chemiosmotic coupling | 20 | 0.0000000 | -0.8137631 | 0.0000000 |
| 860 | MET activates PI3K/AKT signaling | 5 | 0.0026253 | 0.7768482 | 0.0169049 |
| 1093 | PI3K events in ERBB4 signaling | 6 | 0.0015335 | 0.7468285 | 0.0106955 |
| 873 | Malate-aspartate shuttle | 8 | 0.0004343 | -0.7182484 | 0.0036798 |
| 1014 | Negative regulation of activity of TFAP2 (AP-2) family transcription factors | 6 | 0.0023564 | -0.7168796 | 0.0153804 |
| 1669 | Synthesis of Ketone Bodies | 6 | 0.0027722 | -0.7052699 | 0.0176179 |
| 1213 | Purine ribonucleoside monophosphate biosynthesis | 9 | 0.0003045 | -0.6950937 | 0.0026743 |
| 882 | Maturation of spike protein_9683686 | 5 | 0.0071580 | -0.6944621 | 0.0385216 |
| 811 | Ketone body metabolism | 8 | 0.0007267 | -0.6898731 | 0.0057776 |
| 933 | Mitochondrial translation elongation | 90 | 0.0000000 | -0.6894660 | 0.0000000 |
| 1127 | Peptide chain elongation | 88 | 0.0000000 | -0.6817663 | 0.0000000 |
| 934 | Mitochondrial translation initiation | 90 | 0.0000000 | -0.6774689 | 0.0000000 |
| 1867 | Viral mRNA Translation | 88 | 0.0000000 | -0.6691108 | 0.0000000 |
| 310 | Cristae formation | 33 | 0.0000000 | -0.6654582 | 0.0000000 |
| 495 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.6644981 | 0.0000000 |
| 291 | Complex III assembly | 23 | 0.0000000 | -0.6616507 | 0.0000009 |
| 935 | Mitochondrial translation termination | 90 | 0.0000000 | -0.6604064 | 0.0000000 |
| 497 | Eukaryotic Translation Termination | 92 | 0.0000000 | -0.6569600 | 0.0000000 |
| 1487 | SRP-dependent cotranslational protein targeting to membrane | 111 | 0.0000000 | -0.6547822 | 0.0000000 |
| 559 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.6511740 | 0.0000000 |
| 1514 | Selenocysteine synthesis | 92 | 0.0000000 | -0.6491116 | 0.0000000 |
| 1454 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.6478522 | 0.0000000 |
| 1666 | Synthesis of GDP-mannose | 6 | 0.0060170 | -0.6475091 | 0.0330252 |
| 1039 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 94 | 0.0000000 | -0.6441549 | 0.0000000 |
| 932 | Mitochondrial translation | 96 | 0.0000000 | -0.6410043 | 0.0000000 |
| 930 | Mitochondrial protein import | 63 | 0.0000000 | -0.6387210 | 0.0000000 |
| 1055 | Nucleotide biosynthesis | 12 | 0.0001578 | -0.6298570 | 0.0014942 |
| 815 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.6233858 | 0.0000000 |
| 1415 | Release of apoptotic factors from the mitochondria | 6 | 0.0084707 | -0.6206066 | 0.0441421 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_eos_a_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa50b83feb.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- crp_eos_b_adj
myname <- "crp_eos_b_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 1127 | Peptide chain elongation | 88 | 0.0000000 | -0.8467613 | 0.0000000 |
| 559 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.8436203 | 0.0000000 |
| 495 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.8382640 | 0.0000000 |
| 1867 | Viral mRNA Translation | 88 | 0.0000000 | -0.8311112 | 0.0000000 |
| 1454 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.8200812 | 0.0000000 |
| 1514 | Selenocysteine synthesis | 92 | 0.0000000 | -0.8080562 | 0.0000000 |
| 815 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.8017502 | 0.0000000 |
| 220 | Cap-dependent Translation Initiation | 118 | 0.0000000 | -0.8001974 | 0.0000000 |
| 496 | Eukaryotic Translation Initiation | 118 | 0.0000000 | -0.8001974 | 0.0000000 |
| 619 | GTP hydrolysis and joining of the 60S ribosomal subunit | 111 | 0.0000000 | -0.7993619 | 0.0000000 |
| 497 | Eukaryotic Translation Termination | 92 | 0.0000000 | -0.7940265 | 0.0000000 |
| 572 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | -0.7819266 | 0.0000000 |
| 1143 | Phosphate bond hydrolysis by NUDT proteins | 7 | 0.0003964 | -0.7730863 | 0.0032729 |
| 1039 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 94 | 0.0000000 | -0.7669696 | 0.0000000 |
| 1433 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 100 | 0.0000000 | -0.7547651 | 0.0000000 |
| 1487 | SRP-dependent cotranslational protein targeting to membrane | 111 | 0.0000000 | -0.7528063 | 0.0000000 |
| 73 | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 59 | 0.0000000 | -0.7360135 | 0.0000000 |
| 360 | Defective GALNT3 causes HFTC | 9 | 0.0001377 | 0.7337275 | 0.0013239 |
| 1445 | Ribosomal scanning and start codon recognition | 58 | 0.0000000 | -0.7322144 | 0.0000000 |
| 1803 | Translation initiation complex formation | 58 | 0.0000000 | -0.7315261 | 0.0000000 |
| 1891 | Zygotic genome activation (ZGA) | 5 | 0.0048468 | 0.7274166 | 0.0269079 |
| 550 | Formation of ATP by chemiosmotic coupling | 20 | 0.0000000 | -0.7152555 | 0.0000005 |
| 1363 | Regulation of NFE2L2 gene expression | 8 | 0.0004989 | 0.7106998 | 0.0039502 |
| 934 | Mitochondrial translation initiation | 90 | 0.0000000 | -0.6964748 | 0.0000000 |
| 1513 | Selenoamino acid metabolism | 115 | 0.0000000 | -0.6956546 | 0.0000000 |
| 1304 | RUNX1 regulates transcription of genes involved in WNT signaling | 5 | 0.0072644 | 0.6931891 | 0.0364587 |
| 1460 | SARS-CoV-2 modulates host translation machinery | 49 | 0.0000000 | -0.6889108 | 0.0000000 |
| 1333 | Reelin signalling pathway | 5 | 0.0082385 | 0.6822588 | 0.0393979 |
| 935 | Mitochondrial translation termination | 90 | 0.0000000 | -0.6820738 | 0.0000000 |
| 933 | Mitochondrial translation elongation | 90 | 0.0000000 | -0.6802440 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_eos_b_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa31862fe4.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- crp_pod1_a_adj
myname <- "crp_pod1_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 854 | MET activates PI3K/AKT signaling | 5 | 0.0013897 | 0.8254518 | 0.0087816 |
| 178 | CD163 mediating an anti-inflammatory response | 8 | 0.0000618 | 0.8177571 | 0.0006980 |
| 962 | NFE2L2 regulates pentose phosphate pathway genes | 8 | 0.0001500 | 0.7738997 | 0.0013724 |
| 278 | Cohesin Loading onto Chromatin | 10 | 0.0000309 | 0.7608342 | 0.0004198 |
| 749 | Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 6 | 0.0022889 | 0.7189407 | 0.0132044 |
| 484 | Establishment of Sister Chromatid Cohesion | 11 | 0.0000932 | 0.6803075 | 0.0009428 |
| 1501 | Scavenging by Class A Receptors | 10 | 0.0003150 | 0.6578355 | 0.0025643 |
| 856 | MET activates RAP1 and RAC1 | 10 | 0.0003164 | 0.6576378 | 0.0025643 |
| 1296 | RUNX1 regulates transcription of genes involved in BCR signaling | 6 | 0.0069065 | 0.6367801 | 0.0320467 |
| 25 | ATF6 (ATF6-alpha) activates chaperone genes | 10 | 0.0007210 | 0.6174646 | 0.0049908 |
| 614 | Gain-of-function MRAS complexes activate RAF signaling | 8 | 0.0028710 | 0.6086256 | 0.0157579 |
| 1467 | SHOC2 M1731 mutant abolishes MRAS complex function | 8 | 0.0028710 | 0.6086256 | 0.0157579 |
| 1578 | Signaling by MRAS-complex mutants | 8 | 0.0028710 | 0.6086256 | 0.0157579 |
| 21 | APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway | 7 | 0.0053792 | -0.6074690 | 0.0259633 |
| 480 | Erythropoietin activates Phosphoinositide-3-kinase (PI3K) | 11 | 0.0006334 | 0.5949106 | 0.0044571 |
| 1483 | STAT5 activation downstream of FLT3 ITD mutants | 9 | 0.0020101 | 0.5945208 | 0.0120295 |
| 307 | Cross-presentation of particulate exogenous antigens (phagosomes) | 8 | 0.0037808 | 0.5912097 | 0.0195766 |
| 479 | Erythrocytes take up oxygen and release carbon dioxide | 7 | 0.0068353 | 0.5903094 | 0.0318702 |
| 1390 | Regulation of gene expression by Hypoxia-inducible Factor | 8 | 0.0045931 | 0.5786303 | 0.0226822 |
| 442 | EGFR Transactivation by Gastrin | 7 | 0.0092125 | 0.5683356 | 0.0403125 |
| 1563 | Signaling by FLT3 ITD and TKD mutants | 15 | 0.0001384 | 0.5682393 | 0.0012909 |
| 1156 | Platelet sensitization by LDL | 16 | 0.0000890 | 0.5657579 | 0.0009195 |
| 1299 | RUNX1 regulates transcription of genes involved in differentiation of keratinocytes | 7 | 0.0104134 | 0.5591103 | 0.0442570 |
| 939 | Mitotic Telophase/Cytokinesis | 13 | 0.0004956 | 0.5578734 | 0.0036071 |
| 1347 | Regulation of IFNG signaling | 14 | 0.0003033 | 0.5575458 | 0.0024985 |
| 1083 | PI-3K cascade:FGFR3 | 10 | 0.0030974 | 0.5401403 | 0.0166669 |
| 598 | GAB1 signalosome | 14 | 0.0005514 | 0.5331634 | 0.0039824 |
| 871 | Maturation of hRSV A proteins | 13 | 0.0010328 | 0.5255758 | 0.0068178 |
| 419 | Displacement of DNA glycosylase by APEX1 | 9 | 0.0064252 | -0.5245716 | 0.0304009 |
| 1066 | Organic cation transport | 8 | 0.0103885 | 0.5231819 | 0.0442490 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_pod1_a_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa2a9f7237.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- crp_pod1_b_adj
myname <- "crp_pod1_b_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 479 | Erythrocytes take up oxygen and release carbon dioxide | 7 | 0.0002446 | 0.8004330 | 0.0038521 |
| 165 | Biosynthesis of Lipoxins (LX) | 6 | 0.0018909 | 0.7323544 | 0.0194251 |
| 1192 | Propionyl-CoA catabolism | 5 | 0.0052667 | -0.7205008 | 0.0432223 |
| 375 | Defects of platelet adhesion to exposed collagen | 6 | 0.0062418 | 0.6446714 | 0.0491411 |
| 356 | Defective GALNT3 causes HFTC | 8 | 0.0022059 | 0.6249117 | 0.0217310 |
| 178 | CD163 mediating an anti-inflammatory response | 8 | 0.0031146 | 0.6035185 | 0.0279584 |
| 355 | Defective GALNT12 causes CRCS1 | 8 | 0.0036107 | 0.5941516 | 0.0316723 |
| 1739 | Termination of O-glycan biosynthesis | 15 | 0.0001145 | 0.5751828 | 0.0019133 |
| 910 | Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane | 12 | 0.0008449 | 0.5563925 | 0.0108463 |
| 1814 | Transport of connexons to the plasma membrane | 12 | 0.0008449 | 0.5563925 | 0.0108463 |
| 1181 | Processing and activation of SUMO | 10 | 0.0039175 | -0.5267806 | 0.0340123 |
| 180 | CD22 mediated BCR regulation | 58 | 0.0000000 | 0.5163140 | 0.0000000 |
| 408 | Diseases of branched-chain amino acid catabolism | 13 | 0.0013231 | -0.5142836 | 0.0148638 |
| 1413 | Repression of WNT target genes | 14 | 0.0008921 | 0.5128100 | 0.0112739 |
| 1670 | Synthesis of PIPs at the late endosome membrane | 11 | 0.0038898 | -0.5026662 | 0.0339650 |
| 1661 | Synthesis of Leukotrienes (LT) and Eoxins (EX) | 15 | 0.0009137 | 0.4944345 | 0.0113778 |
| 1503 | Scavenging of heme from plasma | 70 | 0.0000000 | 0.4724233 | 0.0000000 |
| 618 | Gap junction assembly | 16 | 0.0013961 | 0.4613705 | 0.0153574 |
| 283 | Common Pathway of Fibrin Clot Formation | 13 | 0.0043315 | 0.4569607 | 0.0365118 |
| 1149 | Plasma lipoprotein remodeling | 18 | 0.0008469 | 0.4542658 | 0.0108463 |
| 271 | Classical antibody-mediated complement activation | 69 | 0.0000000 | 0.4468549 | 0.0000000 |
| 55 | Activation of Matrix Metalloproteinases | 20 | 0.0006118 | 0.4425093 | 0.0086419 |
| 315 | Cytochrome c-mediated apoptotic response | 13 | 0.0059364 | -0.4406780 | 0.0469812 |
| 1799 | Translesion synthesis by POLI | 17 | 0.0022622 | -0.4277199 | 0.0220589 |
| 567 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000002 | -0.4208593 | 0.0000060 |
| 1800 | Translesion synthesis by POLK | 17 | 0.0026846 | -0.4204736 | 0.0252797 |
| 141 | BBSome-mediated cargo-targeting to cilium | 23 | 0.0005187 | -0.4180385 | 0.0075490 |
| 1793 | Translation initiation complex formation | 58 | 0.0000000 | -0.4172389 | 0.0000013 |
| 72 | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 59 | 0.0000000 | -0.4163043 | 0.0000011 |
| 159 | Binding and Uptake of Ligands by Scavenger Receptors | 90 | 0.0000000 | 0.4153297 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/crp_pod1_b_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa7c5ae47c.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- dex_crplo_t0_adj
myname <- "dex_crplo_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 164 | Biosynthesis of EPA-derived SPMs | 6 | 0.0002574 | 0.8614770 | 0.0043894 |
| 165 | Biosynthesis of Lipoxins (LX) | 6 | 0.0003349 | 0.8454232 | 0.0052516 |
| 163 | Biosynthesis of E-series 18(S)-resolvins | 5 | 0.0011742 | 0.8379145 | 0.0135495 |
| 1206 | Protein repair | 6 | 0.0009267 | 0.7806745 | 0.0115035 |
| 309 | Cross-presentation of particulate exogenous antigens (phagosomes) | 8 | 0.0002058 | 0.7577303 | 0.0036382 |
| 1658 | Synthesis of 15-eicosatetraenoic acid derivatives | 6 | 0.0027106 | 0.7068850 | 0.0240705 |
| 1659 | Synthesis of 5-eicosatetraenoic acids | 7 | 0.0015472 | 0.6908802 | 0.0164719 |
| 1657 | Synthesis of 12-eicosatetraenoic acid derivatives | 6 | 0.0050614 | 0.6607666 | 0.0399723 |
| 1105 | POLB-Dependent Long Patch Base Excision Repair | 8 | 0.0012729 | -0.6577738 | 0.0142434 |
| 1532 | Signal attenuation | 9 | 0.0006861 | 0.6534671 | 0.0090557 |
| 777 | Interleukin-21 signaling | 9 | 0.0011813 | -0.6242726 | 0.0135500 |
| 1062 | OAS antiviral response | 8 | 0.0025811 | -0.6152456 | 0.0232422 |
| 805 | Keratan sulfate degradation | 9 | 0.0031911 | 0.5675709 | 0.0274521 |
| 108 | Antimicrobial peptides | 34 | 0.0000000 | 0.5571883 | 0.0000014 |
| 1417 | Replacement of protamines by nucleosomes in the male pronucleus | 13 | 0.0005306 | 0.5549322 | 0.0074637 |
| 280 | Cohesin Loading onto Chromatin | 10 | 0.0026702 | -0.5484355 | 0.0238671 |
| 1266 | RNA Polymerase I Promoter Opening | 17 | 0.0000926 | 0.5475625 | 0.0022964 |
| 888 | Metabolism of Angiotensinogen to Angiotensins | 12 | 0.0010714 | 0.5452923 | 0.0127446 |
| 942 | Mitotic Telophase/Cytokinesis | 13 | 0.0009218 | -0.5306837 | 0.0115035 |
| 1430 | Response of EIF2AK1 (HRI) to heme deficiency | 14 | 0.0007104 | 0.5225306 | 0.0093119 |
| 987 | NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | 32 | 0.0000005 | -0.5122693 | 0.0000298 |
| 676 | HDR through MMEJ (alt-NHEJ) | 12 | 0.0024670 | -0.5046741 | 0.0224242 |
| 1703 | TGFBR3 expression | 20 | 0.0001038 | -0.5012677 | 0.0025009 |
| 285 | Common Pathway of Fibrin Clot Formation | 13 | 0.0017727 | 0.5006634 | 0.0181418 |
| 1362 | Regulation of NPAS4 gene expression | 11 | 0.0051443 | -0.4871511 | 0.0402970 |
| 42 | Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 | 20 | 0.0005130 | 0.4486430 | 0.0073379 |
| 1674 | Synthesis of PIPs at the early endosome membrane | 16 | 0.0021424 | -0.4432198 | 0.0205092 |
| 1292 | RORA activates gene expression | 18 | 0.0011520 | -0.4424919 | 0.0133729 |
| 1818 | Transport of Ribonucleoproteins into the Host Nucleus | 32 | 0.0000149 | -0.4422595 | 0.0005507 |
| 1666 | Synthesis of Leukotrienes (LT) and Eoxins (EX) | 16 | 0.0022640 | 0.4408346 | 0.0210495 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_crplo_t0_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa10276be0.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- dex_crphi_t0_adj
myname <- "dex_crphi_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 1148 | Phosphorylation of Emi1 | 6 | 0.0010272 | -0.7738596 | 0.0048043 |
| 273 | Classical antibody-mediated complement activation | 70 | 0.0000000 | -0.7615138 | 0.0000000 |
| 983 | NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose | 5 | 0.0038200 | -0.7469380 | 0.0146927 |
| 1508 | Scavenging of heme from plasma | 71 | 0.0000000 | -0.7389633 | 0.0000000 |
| 307 | Creation of C4 and C2 activators | 72 | 0.0000000 | -0.7354141 | 0.0000000 |
| 982 | NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | 8 | 0.0004601 | -0.7151107 | 0.0024358 |
| 879 | Maturation of spike protein_9683686 | 5 | 0.0057699 | -0.7128379 | 0.0204388 |
| 742 | Initial triggering of complement | 80 | 0.0000000 | -0.6919929 | 0.0000000 |
| 507 | FCGR activation | 77 | 0.0000000 | -0.6874154 | 0.0000000 |
| 1662 | Synthesis of GDP-mannose | 6 | 0.0038077 | -0.6821106 | 0.0146750 |
| 180 | CD22 mediated BCR regulation | 59 | 0.0000000 | -0.6782528 | 0.0000000 |
| 659 | Glycosphingolipid transport | 7 | 0.0020856 | -0.6716958 | 0.0089113 |
| 557 | Formation of annular gap junctions | 10 | 0.0002510 | -0.6685361 | 0.0014395 |
| 1010 | Negative regulation of TCF-dependent signaling by DVL-interacting proteins | 5 | 0.0099340 | -0.6657306 | 0.0319580 |
| 1445 | Role of LAT2/NTAL/LAB on calcium mobilization | 78 | 0.0000000 | -0.6453945 | 0.0000000 |
| 1647 | Sulfide oxidation to sulfate | 5 | 0.0125604 | -0.6445278 | 0.0386028 |
| 1837 | Type I hemidesmosome assembly | 8 | 0.0016049 | -0.6440971 | 0.0071422 |
| 406 | Diseases of Base Excision Repair | 5 | 0.0128468 | -0.6424606 | 0.0393219 |
| 984 | NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | 7 | 0.0034402 | -0.6384498 | 0.0134993 |
| 985 | NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake | 5 | 0.0137408 | -0.6362589 | 0.0410520 |
| 1845 | Unwinding of DNA | 12 | 0.0001962 | -0.6207491 | 0.0011706 |
| 660 | Glyoxylate metabolism and glycine degradation | 13 | 0.0001077 | -0.6202167 | 0.0007157 |
| 57 | Activation of NIMA Kinases NEK9, NEK6, NEK7 | 7 | 0.0045039 | -0.6199319 | 0.0168523 |
| 599 | G2/M DNA replication checkpoint | 5 | 0.0169888 | -0.6163732 | 0.0490082 |
| 1446 | Role of phospholipids in phagocytosis | 89 | 0.0000000 | -0.6104542 | 0.0000000 |
| 159 | Binding and Uptake of Ligands by Scavenger Receptors | 93 | 0.0000000 | -0.5991499 | 0.0000000 |
| 1361 | Regulation of NFE2L2 gene expression | 8 | 0.0036774 | -0.5929810 | 0.0142870 |
| 994 | Nef Mediated CD4 Down-regulation | 9 | 0.0021601 | -0.5903918 | 0.0091888 |
| 497 | Expression and translocation of olfactory receptors | 52 | 0.0000000 | 0.5867861 | 0.0000000 |
| 508 | FCGR3A-mediated IL10 synthesis | 100 | 0.0000000 | -0.5835765 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_crphi_t0_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa13dba2fa.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- dex_crplo_eos_adj
myname <- "dex_crplo_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 1301 | RUNX1 regulates expression of components of tight junctions | 5 | 0.0012351 | 0.8341911 | 0.0111508 |
| 22 | APOBEC3G mediated resistance to HIV-1 infection | 5 | 0.0028424 | -0.7705920 | 0.0224146 |
| 180 | CD163 mediating an anti-inflammatory response | 9 | 0.0000763 | 0.7613259 | 0.0010310 |
| 573 | Formation of the ureteric bud | 5 | 0.0032981 | 0.7587706 | 0.0252856 |
| 1303 | RUNX1 regulates transcription of genes involved in BCR signaling | 6 | 0.0014660 | 0.7499053 | 0.0128159 |
| 1141 | Phenylalanine metabolism | 5 | 0.0043226 | -0.7368555 | 0.0301490 |
| 166 | Biosynthesis of Lipoxins (LX) | 6 | 0.0025334 | 0.7117265 | 0.0201417 |
| 1312 | RUNX3 regulates BCL2L11 (BIM) transcription | 5 | 0.0079667 | 0.6851869 | 0.0486472 |
| 1107 | POLB-Dependent Long Patch Base Excision Repair | 8 | 0.0009281 | -0.6760266 | 0.0086410 |
| 1127 | Peptide chain elongation | 88 | 0.0000000 | -0.6601572 | 0.0000000 |
| 495 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.6528589 | 0.0000000 |
| 559 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.6440203 | 0.0000000 |
| 1454 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.6414905 | 0.0000000 |
| 497 | Eukaryotic Translation Termination | 92 | 0.0000000 | -0.6408553 | 0.0000000 |
| 1867 | Viral mRNA Translation | 88 | 0.0000000 | -0.6407460 | 0.0000000 |
| 1514 | Selenocysteine synthesis | 92 | 0.0000000 | -0.6337502 | 0.0000000 |
| 1039 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 94 | 0.0000000 | -0.5896332 | 0.0000000 |
| 968 | NFE2L2 regulates pentose phosphate pathway genes | 8 | 0.0040572 | 0.5866718 | 0.0288183 |
| 619 | GTP hydrolysis and joining of the 60S ribosomal subunit | 111 | 0.0000000 | -0.5855057 | 0.0000000 |
| 1814 | Translocation of ZAP-70 to Immunological synapse | 24 | 0.0000007 | -0.5851384 | 0.0000163 |
| 815 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.5842852 | 0.0000000 |
| 220 | Cap-dependent Translation Initiation | 118 | 0.0000000 | -0.5833921 | 0.0000000 |
| 496 | Eukaryotic Translation Initiation | 118 | 0.0000000 | -0.5833921 | 0.0000000 |
| 182 | CD22 mediated BCR regulation | 58 | 0.0000000 | 0.5796941 | 0.0000000 |
| 1433 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 100 | 0.0000000 | -0.5728198 | 0.0000000 |
| 572 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | -0.5725226 | 0.0000000 |
| 1510 | Scavenging of heme from plasma | 70 | 0.0000000 | 0.5716097 | 0.0000000 |
| 1460 | SARS-CoV-2 modulates host translation machinery | 49 | 0.0000000 | -0.5654335 | 0.0000000 |
| 1298 | RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) | 9 | 0.0034641 | 0.5626699 | 0.0260415 |
| 549 | Folding of actin by CCT/TriC | 10 | 0.0021536 | -0.5602710 | 0.0174823 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_crplo_eos_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa112b3dce.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- dex_crphi_eos_adj
myname <- "dex_crphi_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 1303 | RUNX1 regulates transcription of genes involved in BCR signaling | 6 | 0.0009997 | 0.7756559 | 0.0257534 |
| 180 | CD163 mediating an anti-inflammatory response | 9 | 0.0000714 | 0.7644081 | 0.0051791 |
| 580 | Fructose metabolism | 7 | 0.0018082 | -0.6809229 | 0.0371641 |
| 984 | NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | 8 | 0.0013068 | -0.6562344 | 0.0293567 |
| 862 | MET activates RAP1 and RAC1 | 10 | 0.0025032 | 0.5520124 | 0.0460594 |
| 25 | ATF6 (ATF6-alpha) activates chaperone genes | 10 | 0.0026565 | 0.5487198 | 0.0479666 |
| 309 | Creation of C4 and C2 activators | 71 | 0.0000000 | -0.4774859 | 0.0000000 |
| 745 | Initial triggering of complement | 79 | 0.0000000 | -0.4725873 | 0.0000000 |
| 1814 | Translocation of ZAP-70 to Immunological synapse | 24 | 0.0000615 | -0.4724232 | 0.0047531 |
| 275 | Classical antibody-mediated complement activation | 69 | 0.0000000 | -0.4676606 | 0.0000000 |
| 1510 | Scavenging of heme from plasma | 70 | 0.0000000 | -0.4449542 | 0.0000001 |
| 344 | DNA strand elongation | 32 | 0.0000948 | -0.3986349 | 0.0057816 |
| 182 | CD22 mediated BCR regulation | 58 | 0.0000002 | -0.3920310 | 0.0000514 |
| 1149 | Phosphorylation of CD3 and TCR zeta chains | 27 | 0.0006386 | -0.3796111 | 0.0203369 |
| 1082 | PD-1 signaling | 28 | 0.0006018 | -0.3745424 | 0.0197053 |
| 924 | Mitochondrial RNA degradation | 25 | 0.0012241 | 0.3735287 | 0.0288463 |
| 693 | Hedgehog ligand biogenesis | 47 | 0.0000112 | 0.3702818 | 0.0011375 |
| 1065 | Olfactory Signaling Pathway | 61 | 0.0000006 | 0.3699367 | 0.0000930 |
| 510 | FCGR activation | 76 | 0.0000000 | -0.3687872 | 0.0000087 |
| 500 | Expression and translocation of olfactory receptors | 56 | 0.0000018 | 0.3685930 | 0.0002345 |
| 989 | NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | 33 | 0.0002705 | -0.3662768 | 0.0118779 |
| 988 | NR1H2 and NR1H3-mediated signaling | 39 | 0.0001191 | -0.3560203 | 0.0063919 |
| 1448 | Role of phospholipids in phagocytosis | 88 | 0.0000000 | -0.3537970 | 0.0000037 |
| 700 | Hh mutants are degraded by ERAD | 42 | 0.0000823 | 0.3510736 | 0.0056812 |
| 699 | Hh mutants abrogate ligand secretion | 43 | 0.0000724 | 0.3496909 | 0.0051791 |
| 27 | AUF1 (hnRNP D0) binds and destabilizes mRNA | 42 | 0.0000909 | 0.3489439 | 0.0057816 |
| 1098 | PINK1-PRKN Mediated Mitophagy | 31 | 0.0008837 | 0.3450209 | 0.0239317 |
| 1387 | Regulation of activated PAK-2p34 by proteasome mediated degradation | 37 | 0.0004111 | 0.3355772 | 0.0154205 |
| 1447 | Role of LAT2/NTAL/LAB on calcium mobilization | 77 | 0.0000004 | -0.3336991 | 0.0000721 |
| 383 | Degradation of GLI1 by the proteasome | 46 | 0.0000958 | 0.3323919 | 0.0057816 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_crphi_eos_adj_mitchreport.rds ".##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa5a2c6b36.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- dex_crplo_pod1_adj
myname <- "dex_crplo_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 484 | Establishment of Sister Chromatid Cohesion | 11 | 0.0000090 | -0.7731595 | 0.0012282 |
| 278 | Cohesin Loading onto Chromatin | 10 | 0.0002333 | -0.6719578 | 0.0144548 |
| 11 | ALK mutants bind TKIs | 11 | 0.0008321 | -0.5818576 | 0.0355209 |
| 1670 | Synthesis of PIPs at the late endosome membrane | 11 | 0.0012751 | -0.5609042 | 0.0471062 |
| 1347 | Regulation of IFNG signaling | 14 | 0.0003423 | -0.5526895 | 0.0199260 |
| 939 | Mitotic Telophase/Cytokinesis | 13 | 0.0010700 | -0.5239751 | 0.0437336 |
| 1669 | Synthesis of PIPs at the early endosome membrane | 16 | 0.0007130 | -0.4886637 | 0.0334051 |
| 759 | Interferon alpha/beta signaling | 63 | 0.0000000 | -0.4161771 | 0.0000070 |
| 722 | Impaired BRCA2 binding to RAD51 | 35 | 0.0000866 | -0.3833511 | 0.0063967 |
| 1151 | Platelet Aggregation (Plug Formation) | 28 | 0.0011224 | 0.3556756 | 0.0445699 |
| 368 | Defective homologous recombination repair (HRR) due to BRCA2 loss of function | 41 | 0.0003846 | -0.3204146 | 0.0211069 |
| 404 | Diseases of DNA Double-Strand Break Repair | 41 | 0.0003846 | -0.3204146 | 0.0211069 |
| 674 | HDR through Single Strand Annealing (SSA) | 37 | 0.0008106 | -0.3181408 | 0.0353903 |
| 1179 | Presynaptic phase of homologous DNA pairing and strand exchange | 40 | 0.0005038 | -0.3178334 | 0.0254708 |
| 840 | M-decay: degradation of maternal mRNAs by maternally stored factors | 41 | 0.0011731 | -0.2928853 | 0.0445699 |
| 697 | Homologous DNA Pairing and Strand Exchange | 43 | 0.0011471 | -0.2865695 | 0.0445699 |
| 717 | ISG15 antiviral mechanism | 72 | 0.0000649 | -0.2721897 | 0.0049903 |
| 97 | Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal | 90 | 0.0000539 | -0.2462421 | 0.0047046 |
| 98 | Amplification of signal from the kinetochores | 90 | 0.0000539 | -0.2462421 | 0.0047046 |
| 1420 | Resolution of Sister Chromatid Cohesion | 115 | 0.0000116 | -0.2366881 | 0.0014846 |
| 938 | Mitotic Spindle Checkpoint | 107 | 0.0000393 | -0.2300384 | 0.0044388 |
| 1521 | Separation of Sister Chromatids | 167 | 0.0000085 | -0.1996063 | 0.0012282 |
| 231 | Cell Cycle Checkpoints | 245 | 0.0000001 | -0.1993538 | 0.0000359 |
| 109 | Antiviral mechanism by IFN-stimulated genes | 140 | 0.0000468 | -0.1992821 | 0.0046883 |
| 446 | EML4 and NUDC in mitotic spindle formation | 106 | 0.0005361 | -0.1946126 | 0.0264044 |
| 1421 | Respiratory Syncytial Virus Infection Pathway | 97 | 0.0009265 | -0.1945801 | 0.0386925 |
| 933 | Mitotic G1 phase and G1/S transition | 138 | 0.0001317 | -0.1884950 | 0.0093699 |
| 594 | G2/M Checkpoints | 126 | 0.0002883 | -0.1870164 | 0.0173087 |
| 935 | Mitotic Metaphase and Anaphase | 211 | 0.0000029 | -0.1868833 | 0.0006141 |
| 932 | Mitotic Anaphase | 210 | 0.0000033 | -0.1862060 | 0.0006330 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_crplo_pod1_adj_mitchreport.rds ".##
##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa67e20185.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEde <- dex_crphi_pod1_adj
myname <- "dex_crphi_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"REACTOME")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 180 | CD22 mediated BCR regulation | 58 | 0.0000000 | -0.8108435 | 0.0000000 |
| 1143 | Phosphorylation of Emi1 | 6 | 0.0009140 | -0.7815849 | 0.0148792 |
| 1503 | Scavenging of heme from plasma | 70 | 0.0000000 | -0.7763112 | 0.0000000 |
| 505 | FCGR activation | 76 | 0.0000000 | -0.7704138 | 0.0000000 |
| 271 | Classical antibody-mediated complement activation | 69 | 0.0000000 | -0.7520565 | 0.0000000 |
| 596 | G2/M DNA replication checkpoint | 5 | 0.0036450 | -0.7507342 | 0.0426950 |
| 1831 | Type I hemidesmosome assembly | 8 | 0.0003992 | -0.7227936 | 0.0076141 |
| 305 | Creation of C4 and C2 activators | 71 | 0.0000000 | -0.7182992 | 0.0000000 |
| 1440 | Role of LAT2/NTAL/LAB on calcium mobilization | 77 | 0.0000000 | -0.6841033 | 0.0000000 |
| 1839 | Unwinding of DNA | 12 | 0.0000607 | -0.6684164 | 0.0015355 |
| 57 | Activation of NIMA Kinases NEK9, NEK6, NEK7 | 7 | 0.0023128 | -0.6649453 | 0.0302238 |
| 739 | Initial triggering of complement | 79 | 0.0000000 | -0.6400613 | 0.0000000 |
| 502 | FCERI mediated Ca+2 mobilization | 92 | 0.0000000 | -0.6254646 | 0.0000000 |
| 506 | FCGR3A-mediated IL10 synthesis | 99 | 0.0000000 | -0.6234845 | 0.0000000 |
| 105 | Antigen activates B Cell Receptor (BCR) leading to generation of second messengers | 83 | 0.0000000 | -0.6229969 | 0.0000000 |
| 1441 | Role of phospholipids in phagocytosis | 88 | 0.0000000 | -0.6219541 | 0.0000000 |
| 874 | Maturation of protein 3a_9683673 | 9 | 0.0020577 | -0.5931819 | 0.0280345 |
| 875 | Maturation of protein 3a_9694719 | 9 | 0.0020577 | -0.5931819 | 0.0280345 |
| 774 | Interleukin-21 signaling | 9 | 0.0020804 | -0.5925542 | 0.0281436 |
| 159 | Binding and Uptake of Ligands by Scavenger Receptors | 90 | 0.0000000 | -0.5894984 | 0.0000000 |
| 283 | Common Pathway of Fibrin Clot Formation | 13 | 0.0003275 | -0.5753803 | 0.0067657 |
| 503 | FCERI mediated MAPK activation | 93 | 0.0000000 | -0.5571437 | 0.0000000 |
| 507 | FCGR3A-mediated phagocytosis | 121 | 0.0000000 | -0.5536220 | 0.0000000 |
| 823 | Leishmania phagocytosis | 121 | 0.0000000 | -0.5536220 | 0.0000000 |
| 1114 | Parasite infection | 121 | 0.0000000 | -0.5536220 | 0.0000000 |
| 1379 | Regulation of actin dynamics for phagocytic cup formation | 123 | 0.0000000 | -0.5387070 | 0.0000000 |
| 592 | G1/S-Specific Transcription | 29 | 0.0000010 | -0.5249197 | 0.0000372 |
| 289 | Condensation of Prometaphase Chromosomes | 11 | 0.0026505 | -0.5233200 | 0.0330393 |
| 1338 | Regulation of Complement cascade | 96 | 0.0000000 | -0.5130522 | 0.0000000 |
| 103 | Anti-inflammatory response favouring Leishmania parasite infection | 131 | 0.0000000 | -0.5129791 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/dex_crphi_pod1_adj_mitchreport.rds ".##
##
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## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa424dc1da.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEMulti-contrast enrichment anslysis.
l2 <- list("crp_t0_a"=crp_t0_a_adj,
"crp t0 b"=crp_t0_b_adj,
"crp eos a"=crp_eos_a_adj,
"crp eos b"=crp_eos_b_adj,
"crp _pod1 a"=crp_pod1_a_adj,
"crp pod1 b"=crp_pod1_b_adj,
"dex crplo t0"=dex_crplo_t0_adj,
"dex crphi t0"=dex_crphi_t0_adj,
"dex crplo eos"=dex_crplo_eos_adj,
"dex crphi eos"=dex_crphi_eos_adj,
"dex crplo pod1"=dex_crplo_pod1_adj,
"dex crphi pod1"=dex_crphi_pod1_adj)
m2 <- mitch_import(x=l2, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21771.6666666667## Note: no. genes in output = 21032## Note: estimated proportion of input genes in output = 0.966mm2 <- mitch_calc(x=m2,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm2$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:15)]
rownames(top) <- top[,1]
top[,1] = NULL
colnames(top) <- gsub("^s\\.","",colnames(top))
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(7,20), cexRow=0.6, cexCol=0.7 )
as.matrix(top) |>
kbl(caption="Top REACTOMEs in multi enrichment analysis") |>
kable_paper("hover", full_width = F)| crp_t0_a | crp.t0.b | crp.eos.a | crp.eos.b | crp._pod1.a | crp.pod1.b | dex.crplo.t0 | dex.crphi.t0 | dex.crplo.eos | dex.crphi.eos | dex.crplo.pod1 | dex.crphi.pod1 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sulfide oxidation to sulfate | -0.7545061 | 0.4949922 | -0.5282827 | -0.5488848 | -0.6024540 | 0.2471584 | 0.5505398 | -0.6383887 | -0.1764493 | -0.5081752 | 0.7342274 | -0.5458411 |
| CD163 mediating an anti-inflammatory response | -0.2419497 | 0.1677725 | 0.0896119 | 0.4071062 | 0.8194207 | 0.6062595 | 0.4283795 | -0.2133157 | 0.8104904 | 0.7892290 | 0.2167880 | 0.3812785 |
| Peptide chain elongation | -0.8125677 | 0.1859676 | -0.6871127 | -0.8502778 | -0.3450059 | -0.3654777 | 0.3634319 | -0.3761944 | -0.6536929 | 0.0018576 | 0.0459567 | 0.0141350 |
| Erythrocytes take up oxygen and release carbon dioxide | 0.4204450 | 0.5443656 | 0.3304433 | 0.5123221 | 0.5928385 | 0.8020588 | 0.4363853 | -0.4130661 | 0.4067063 | 0.6093086 | -0.0558859 | -0.2799728 |
| Biosynthesis of Lipoxins (LX) | -0.3777862 | 0.4643774 | -0.0179143 | 0.3309395 | 0.3733948 | 0.7351057 | 0.8467929 | -0.3733948 | 0.7176036 | 0.4230159 | 0.1980088 | -0.2640540 |
| CD22 mediated BCR regulation | -0.5446693 | 0.3039165 | -0.5283106 | 0.2818234 | -0.3711963 | 0.5136633 | 0.0562282 | -0.6858449 | 0.5826560 | -0.3880501 | 0.1324124 | -0.8074115 |
| Classical antibody-mediated complement activation | -0.6070603 | 0.2339080 | -0.5714095 | 0.2366283 | -0.3006611 | 0.4439880 | 0.0577755 | -0.7702981 | 0.5419697 | -0.4646663 | 0.1338766 | -0.7482140 |
| Scavenging of heme from plasma | -0.5669928 | 0.2725140 | -0.5353193 | 0.2745189 | -0.2961111 | 0.4701223 | 0.0998495 | -0.7465873 | 0.5748396 | -0.4416498 | 0.1206384 | -0.7729015 |
| Eukaryotic Translation Elongation | -0.7937461 | 0.1857523 | -0.6690980 | -0.8412130 | -0.3357273 | -0.3537550 | 0.3476828 | -0.3682187 | -0.6461474 | -0.0055604 | 0.0392768 | -0.0075402 |
| Viral mRNA Translation | -0.8026084 | 0.1654497 | -0.6743063 | -0.8344641 | -0.3144530 | -0.3588473 | 0.3511830 | -0.3616384 | -0.6341244 | 0.0195218 | 0.0192431 | 0.0190707 |
| Cohesin Loading onto Chromatin | 0.1660927 | -0.6739416 | 0.6198364 | 0.4809343 | 0.7625630 | -0.4166968 | -0.5487680 | -0.0163733 | 0.1694606 | 0.1614499 | -0.6715156 | 0.0930549 |
| Formation of a pool of free 40S subunits | -0.7830384 | 0.1420998 | -0.6549617 | -0.8461962 | -0.2844347 | -0.4003321 | 0.3382832 | -0.3544792 | -0.6368539 | 0.0320595 | 0.0164397 | 0.0378249 |
| SARS-CoV-1 modulates host translation machinery | -0.7824612 | 0.1985881 | -0.6437866 | -0.8169863 | -0.3477355 | -0.3338467 | 0.3547924 | -0.3464602 | -0.6330492 | 0.0455775 | 0.0399679 | -0.0036674 |
| Eukaryotic Translation Termination | -0.7785920 | 0.1620907 | -0.6615714 | -0.7964013 | -0.3190822 | -0.3653619 | 0.3104394 | -0.3567600 | -0.6342073 | 0.0174289 | 0.0155229 | 0.0107791 |
| Creation of C4 and C2 activators | -0.5891995 | 0.2241008 | -0.5416045 | 0.2122153 | -0.2974144 | 0.4103221 | 0.0575436 | -0.7429062 | 0.5140145 | -0.4746330 | 0.1374514 | -0.7140458 |
| Selenocysteine synthesis | -0.7633183 | 0.1564065 | -0.6536601 | -0.8105090 | -0.3218456 | -0.3698738 | 0.3082827 | -0.3558533 | -0.6268249 | 0.0030872 | 0.0162324 | 0.0209259 |
| Formation of ATP by chemiosmotic coupling | -0.7949933 | 0.0566914 | -0.8110461 | -0.7102132 | 0.1571864 | -0.2972492 | 0.4226870 | -0.5712069 | -0.2826813 | 0.1463497 | 0.0369027 | 0.0303779 |
| Phosphorylation of Emi1 | -0.3700181 | 0.1144456 | -0.3859032 | 0.3339992 | -0.1590253 | 0.6344684 | -0.3729509 | -0.7697137 | 0.2913853 | -0.4467960 | -0.0671867 | -0.7811598 |
| Fructose metabolism | -0.6619806 | 0.2944726 | -0.2563547 | -0.3798403 | -0.4615933 | -0.3622151 | 0.4716630 | -0.3365721 | -0.2656497 | -0.6766027 | 0.6105317 | 0.2847698 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.7615059 | 0.1435655 | -0.6483950 | -0.7688565 | -0.3021983 | -0.3551232 | 0.3015092 | -0.3495135 | -0.5822253 | 0.0354019 | 0.0162269 | 0.0231173 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.7470130 | 0.0927363 | -0.6260794 | -0.8031156 | -0.2257114 | -0.4060213 | 0.3342948 | -0.3319691 | -0.5761514 | 0.0547455 | -0.0162829 | 0.0421927 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.7325834 | 0.0838413 | -0.6228033 | -0.8006266 | -0.2132779 | -0.4033849 | 0.3255599 | -0.3164394 | -0.5773992 | 0.0610093 | -0.0224157 | 0.0437643 |
| Cap-dependent Translation Initiation | -0.7175331 | 0.0864006 | -0.6163241 | -0.8011643 | -0.2145440 | -0.3914031 | 0.3284148 | -0.3228015 | -0.5752274 | 0.0523687 | -0.0046149 | 0.0434240 |
| Eukaryotic Translation Initiation | -0.7175331 | 0.0864006 | -0.6163241 | -0.8011643 | -0.2145440 | -0.3914031 | 0.3284148 | -0.3228015 | -0.5752274 | 0.0523687 | -0.0046149 | 0.0434240 |
| FCGR activation | -0.5416278 | 0.2091896 | -0.4378928 | 0.3015756 | -0.2555525 | 0.3911291 | 0.0434916 | -0.6920488 | 0.4979065 | -0.3641444 | 0.0254038 | -0.7671028 |
| SRP-dependent cotranslational protein targeting to membrane | -0.7526058 | 0.0568771 | -0.6579972 | -0.7531185 | -0.1997263 | -0.3831739 | 0.3132831 | -0.3599343 | -0.5357510 | 0.0936570 | -0.0594624 | -0.0510633 |
| Fructose catabolism | -0.5632282 | 0.4345746 | -0.2395301 | -0.3511961 | -0.4317401 | -0.2436391 | 0.6637086 | -0.2040139 | -0.0863937 | -0.6086365 | 0.6035193 | 0.3181529 |
| Establishment of Sister Chromatid Cohesion | 0.1440248 | -0.6911746 | 0.3358849 | 0.3256354 | 0.6824215 | -0.4116187 | -0.4671735 | -0.0020196 | 0.2428870 | 0.0274747 | -0.7725910 | -0.1274440 |
| G2/M DNA replication checkpoint | -0.4509726 | -0.2228849 | -0.2255671 | 0.1675655 | 0.3647025 | 0.5400200 | -0.1401912 | -0.6120417 | 0.5924859 | -0.1351691 | -0.3612784 | -0.7501879 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.7169893 | 0.1514447 | -0.6232472 | -0.7559592 | -0.2503094 | -0.3326954 | 0.3473058 | -0.3133620 | -0.5649371 | 0.0240860 | 0.0154514 | 0.0098511 |
| NFE2L2 regulates pentose phosphate pathway genes | -0.3371623 | 0.2299634 | 0.4170947 | 0.4181887 | 0.7758633 | 0.4873716 | 0.2602502 | -0.4748383 | 0.5950461 | 0.3722294 | 0.2340777 | 0.1058433 |
| Initial triggering of complement | -0.5456568 | 0.2305282 | -0.5127116 | 0.1644836 | -0.2809402 | 0.3753423 | 0.0603324 | -0.6967533 | 0.4472422 | -0.4692526 | 0.1428758 | -0.6350957 |
| Protein repair | -0.6190589 | 0.0015378 | -0.1150322 | -0.1028885 | 0.4722249 | 0.1703129 | 0.7825232 | -0.2928913 | 0.5411871 | 0.4330194 | 0.0329592 | -0.5610355 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.6965434 | 0.0761483 | -0.5713134 | -0.7781784 | -0.1982363 | -0.4180879 | 0.3084238 | -0.2897365 | -0.5632108 | 0.0863087 | -0.0426726 | 0.0371737 |
| Defective binding of VWF variant to GPIb:IX:V | 0.2089789 | 0.2105959 | -0.2830932 | -0.4077139 | 0.2028345 | 0.5959481 | 0.3907643 | 0.0810862 | 0.5490179 | 0.4406430 | 0.7476197 | -0.3900604 |
| Enhanced binding of GP1BA variant to VWF multimer:collagen | 0.2089789 | 0.2105959 | -0.2830932 | -0.4077139 | 0.2028345 | 0.5959481 | 0.3907643 | 0.0810862 | 0.5490179 | 0.4406430 | 0.7476197 | -0.3900604 |
| NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake | -0.6387502 | 0.0837495 | -0.2332525 | -0.3348552 | -0.0784040 | 0.2864222 | -0.2401389 | -0.6304371 | -0.3628383 | -0.2973225 | 0.6832644 | 0.3657488 |
| Role of LAT2/NTAL/LAB on calcium mobilization | -0.5197142 | 0.1809192 | -0.4006628 | 0.2925842 | -0.2036435 | 0.3157066 | 0.0731118 | -0.6484639 | 0.5091244 | -0.3285104 | 0.0182274 | -0.6795542 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.6781495 | 0.0270283 | -0.5499411 | -0.7320445 | -0.1406902 | -0.4136093 | 0.3097097 | -0.2845361 | -0.4856292 | 0.1018105 | -0.0475874 | 0.0689902 |
| Modulation by Mtb of host immune system | -0.8151045 | -0.0349992 | -0.4537252 | -0.6214574 | 0.1229760 | -0.2785052 | 0.4998607 | -0.2806659 | 0.0020044 | 0.4609411 | -0.1456701 | -0.0266282 |
| Translation initiation complex formation | -0.6740414 | 0.0296508 | -0.5467327 | -0.7274885 | -0.1381415 | -0.4145543 | 0.3027377 | -0.2867803 | -0.4873259 | 0.1089263 | -0.0610378 | 0.0593280 |
| Ribosomal scanning and start codon recognition | -0.6662239 | 0.0269513 | -0.5559642 | -0.7281971 | -0.1250760 | -0.4083726 | 0.2987755 | -0.2754165 | -0.4868852 | 0.1119909 | -0.0600645 | 0.0703465 |
| Phosphate bond hydrolysis by NUDT proteins | -0.7170036 | -0.1221743 | -0.5332224 | -0.7682215 | -0.0642297 | -0.4846815 | 0.2694276 | -0.1544896 | -0.0441855 | 0.2996093 | -0.1991031 | 0.0517819 |
| NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | -0.5695277 | 0.1899853 | -0.2834142 | 0.0876617 | -0.0164574 | 0.3894359 | -0.2341253 | -0.7106283 | -0.3077792 | -0.6514579 | 0.3870576 | 0.0995291 |
| SARS-CoV-2 modulates host translation machinery | -0.6054649 | 0.1771162 | -0.5917084 | -0.6844812 | -0.2600930 | -0.2685527 | 0.2852562 | -0.2885669 | -0.5566304 | 0.0149013 | 0.0417977 | 0.0058755 |
| Selenoamino acid metabolism | -0.6608402 | 0.0921778 | -0.5610773 | -0.6952167 | -0.2299648 | -0.3152183 | 0.2569633 | -0.3057486 | -0.5207594 | 0.0335386 | -0.0073176 | 0.0512351 |
| Type I hemidesmosome assembly | -0.2403682 | 0.1955028 | -0.0031155 | 0.4687619 | 0.1227407 | 0.5536411 | -0.0888271 | -0.6382230 | -0.1166167 | -0.4762890 | 0.0842965 | -0.7222222 |
| Mitochondrial translation elongation | -0.5637772 | 0.0983202 | -0.6863422 | -0.6750188 | -0.1960048 | -0.3562018 | 0.1953140 | -0.3690701 | -0.4598213 | 0.0665616 | -0.0071223 | -0.0871582 |
| Synthesis of PIPs at the late endosome membrane | 0.3690898 | -0.6200596 | 0.3203766 | 0.2172935 | 0.3845375 | -0.5007676 | -0.3510299 | 0.3139934 | 0.4140924 | 0.0346883 | -0.5601455 | 0.1897280 |
| Mitochondrial translation initiation | -0.5407040 | 0.0718461 | -0.6742357 | -0.6913645 | -0.2064506 | -0.3705239 | 0.1743142 | -0.3467259 | -0.4661552 | 0.0722259 | -0.0241789 | -0.1092573 |
mitch_report(res=mm2,outfile="multireactomestratified_all_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpsiUaL8/multireactomestratified_all_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
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## 6/36 [metrics]
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## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]## 11/36
## 12/36 [input_geneset_metrics1]
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## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]
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## 21/36 [heatmap]## 22/36
## 23/36 [effectsize]
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## 31/36 [detailed_geneset_reports2d]## 32/36
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## 35/36 [session_info]
## 36/36## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpsiUaL8/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpsiUaL8/rmarkdown-strd7caa2566fea0.html##
## Output created: /tmp/RtmpsiUaL8/mitch_report.html## [1] TRUEThis might work better if we work on each timepoint separately.
l2 <- list("crp_t0_a"=crp_t0_a_adj, "crp t0 b"=crp_t0_b_adj,
"dex crplo t0"=dex_crplo_t0_adj, "dex crphi t0"=dex_crphi_t0_adj)
m2 <- mitch_import(x=l2, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mm2 <- mitch_calc(x=m2,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm2$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:7)]
rownames(top) <- top[,1]
top[,1] = NULL
colnames(top) <- gsub("^s\\.","",colnames(top))
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(7,20), cexRow=0.6, cexCol=0.7 )
as.matrix(top) |>
kbl(caption="Top REACTOMEs in multi enrichment analysis stratified t0") |>
kable_paper("hover", full_width = F)| crp_t0_a | crp.t0.b | dex.crplo.t0 | dex.crphi.t0 | |
|---|---|---|---|---|
| Biosynthesis of Lipoxins (LX) | -0.3868155 | 0.4633035 | 0.8454232 | -0.3817996 |
| NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose | -0.6481683 | 0.3623051 | -0.2136657 | -0.7469380 |
| Formation of ATP by chemiosmotic coupling | -0.7990618 | 0.0544211 | 0.4209474 | -0.5772586 |
| Protein repair | -0.6253964 | -0.0012197 | 0.7806745 | -0.3024759 |
| Biosynthesis of E-series 18(S)-resolvins | -0.3304368 | 0.3749828 | 0.8379145 | -0.3230826 |
| Formation of annular gap junctions | -0.7470997 | 0.1116926 | 0.1898902 | -0.6685361 |
| Glycosphingolipid transport | -0.7715776 | 0.0083442 | 0.0216478 | -0.6716958 |
| Modulation by Mtb of host immune system | -0.8192118 | -0.0374605 | 0.4977555 | -0.2874851 |
| Classical antibody-mediated complement activation | -0.5813775 | 0.2414050 | 0.0529607 | -0.7615138 |
| Peptide chain elongation | -0.8159421 | 0.1840468 | 0.3611194 | -0.3851306 |
| Viral mRNA Translation | -0.8061612 | 0.1635289 | 0.3489186 | -0.3707093 |
| NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | -0.5768685 | 0.1882948 | -0.2344593 | -0.7151107 |
| Eukaryotic Translation Elongation | -0.7971158 | 0.1838213 | 0.3454204 | -0.3770389 |
| Scavenging of heme from plasma | -0.5430957 | 0.2789035 | 0.0936449 | -0.7389633 |
| Biosynthesis of EPA-derived SPMs | -0.1458257 | 0.3767075 | 0.8614770 | -0.1085651 |
| Creation of C4 and C2 activators | -0.5648709 | 0.2315783 | 0.0528744 | -0.7354141 |
| PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 | -0.6469105 | 0.3038135 | 0.2865326 | -0.5637386 |
| SARS-CoV-1 modulates host translation machinery | -0.7859506 | 0.1967574 | 0.3526406 | -0.3557042 |
| Phosphorylation of Emi1 | -0.3787505 | 0.1116142 | -0.3726826 | -0.7738596 |
| Formation of a pool of free 40S subunits | -0.7868520 | 0.1401777 | 0.3360113 | -0.3633937 |
| Fructose metabolism | -0.6673702 | 0.2927516 | 0.4697891 | -0.3434701 |
| Formyl peptide receptors bind formyl peptides and many other ligands | -0.6187035 | -0.2694637 | 0.5606014 | -0.3120798 |
| Eukaryotic Translation Termination | -0.7823198 | 0.1601790 | 0.3082882 | -0.3657869 |
| Diseases of Mismatch Repair (MMR) | 0.2592362 | -0.6835491 | -0.5528562 | 0.0673131 |
| Selenocysteine synthesis | -0.7670303 | 0.1543785 | 0.3061519 | -0.3647293 |
| Erythrocytes take up oxygen and release carbon dioxide | 0.4129155 | 0.5430636 | 0.4344522 | -0.4182997 |
| CD22 mediated BCR regulation | -0.5156899 | 0.3109448 | 0.0506252 | -0.6782528 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.7653537 | 0.1416000 | 0.2994049 | -0.3584136 |
| Prevention of phagosomal-lysosomal fusion | -0.6614976 | 0.1074415 | 0.2847943 | -0.5366177 |
| Initial triggering of complement | -0.5257802 | 0.2369791 | 0.0559637 | -0.6919929 |
| Nef Mediated CD4 Down-regulation | -0.6541990 | 0.1736781 | 0.0548465 | -0.5903918 |
| SRP-dependent cotranslational protein targeting to membrane | -0.7565032 | 0.0546766 | 0.3111230 | -0.3686723 |
| Glyoxylate metabolism and glycine degradation | -0.5336893 | 0.2109129 | 0.3005304 | -0.6202167 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.7511447 | 0.0906423 | 0.3320345 | -0.3407986 |
| VLDLR internalisation and degradation | -0.6602029 | 0.1635171 | 0.1365393 | -0.5604423 |
| FCGR activation | -0.5211831 | 0.2164409 | 0.0393710 | -0.6874154 |
| Cohesin Loading onto Chromatin | 0.1552608 | -0.6765142 | -0.5484355 | -0.0269716 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.7211822 | 0.1495424 | 0.3450772 | -0.3223457 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.7368499 | 0.0817438 | 0.3233255 | -0.3252507 |
| NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | -0.3966845 | 0.0672434 | -0.4349096 | -0.6384498 |
| Pentose phosphate pathway | -0.6339705 | -0.0635002 | 0.3574387 | -0.4668844 |
| SUMO is conjugated to E1 (UBA2:SAE1) | -0.6688772 | -0.4728013 | -0.0018751 | -0.2822868 |
| Cap-dependent Translation Initiation | -0.7219898 | 0.0842972 | 0.3262334 | -0.3316336 |
| Eukaryotic Translation Initiation | -0.7219898 | 0.0842972 | 0.3262334 | -0.3316336 |
| Synthesis of PIPs at the late endosome membrane | 0.3589243 | -0.6226559 | -0.3514883 | 0.3058819 |
| Synthesis of 5-eicosatetraenoic acids | -0.2730445 | 0.3411962 | 0.6908802 | -0.2536641 |
| Retrograde neurotrophin signalling | -0.5940388 | 0.0922393 | 0.1446457 | -0.5821515 |
| Regulation of NFE2L2 gene expression | 0.0365360 | 0.4139260 | -0.4437151 | -0.5929810 |
| Establishment of Sister Chromatid Cohesion | 0.1342863 | -0.6938394 | -0.4669473 | -0.0117904 |
| Role of LAT2/NTAL/LAB on calcium mobilization | -0.4999871 | 0.1886907 | 0.0681419 | -0.6453945 |
#mitch_report(res=mm2,outfile="multireactomestratified_t0_mitchreport.html",overwrite=TRUE)
l2 <- list("crp_eos_a"=crp_eos_a_adj, "crp eos b"=crp_eos_b_adj,
"dex crplo eos"=dex_crplo_eos_adj, "dex crphi eos"=dex_crphi_eos_adj)
m2 <- mitch_import(x=l2, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mm2 <- mitch_calc(x=m2,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm2$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:7)]
rownames(top) <- top[,1]
top[,1] = NULL
colnames(top) <- gsub("^s\\.","",colnames(top))
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(7,20), cexRow=0.6, cexCol=0.7 )
as.matrix(top) |>
kbl(caption="Top REACTOMEs in multi enrichment analysis stratified EOS") |>
kable_paper("hover", full_width = F)| crp_eos_a | crp.eos.b | dex.crplo.eos | dex.crphi.eos | |
|---|---|---|---|---|
| RUNX1 regulates transcription of genes involved in BCR signaling | 0.5562679 | 0.5473711 | 0.7499053 | 0.7756559 |
| Peptide chain elongation | -0.6817663 | -0.8467613 | -0.6601572 | -0.0088042 |
| Formation of xylulose-5-phosphate | -0.5771392 | -0.6573247 | -0.5937437 | -0.6981177 |
| Eukaryotic Translation Elongation | -0.6644981 | -0.8382640 | -0.6528589 | -0.0159499 |
| Formation of a pool of free 40S subunits | -0.6511740 | -0.8436203 | -0.6440203 | 0.0213590 |
| Viral mRNA Translation | -0.6691108 | -0.8311112 | -0.6407460 | 0.0086434 |
| SARS-CoV-1 modulates host translation machinery | -0.6478522 | -0.8200812 | -0.6414905 | 0.0368701 |
| Selenocysteine synthesis | -0.6491116 | -0.8080562 | -0.6337502 | -0.0075110 |
| Eukaryotic Translation Termination | -0.6569600 | -0.7940265 | -0.6408553 | 0.0066993 |
| Phenylalanine metabolism | -0.4336092 | -0.5974720 | -0.7368555 | -0.5580613 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.6233858 | -0.8017502 | -0.5842852 | 0.0441558 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.6201983 | -0.7993619 | -0.5855057 | 0.0503587 |
| Cap-dependent Translation Initiation | -0.6142408 | -0.8001974 | -0.5833921 | 0.0419039 |
| Eukaryotic Translation Initiation | -0.6142408 | -0.8001974 | -0.5833921 | 0.0419039 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.6441549 | -0.7669696 | -0.5896332 | 0.0245548 |
| MET activates PI3K/AKT signaling | 0.7768482 | 0.3518596 | 0.5666273 | 0.5409293 |
| SRP-dependent cotranslational protein targeting to membrane | -0.6547822 | -0.7528063 | -0.5445248 | 0.0826279 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.6197954 | -0.7547651 | -0.5728198 | 0.0136372 |
| Formation of ATP by chemiosmotic coupling | -0.8137631 | -0.7152555 | -0.2941353 | 0.1376041 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.5757244 | -0.7819266 | -0.5725226 | 0.0777292 |
| CD163 mediating an anti-inflammatory response | 0.0480623 | 0.2985701 | 0.7613259 | 0.7644081 |
| Mitochondrial translation initiation | -0.6774689 | -0.6964748 | -0.4755052 | 0.0641380 |
| Mitochondrial translation elongation | -0.6894660 | -0.6802440 | -0.4692197 | 0.0585178 |
| SARS-CoV-2 modulates host translation machinery | -0.5956878 | -0.6889108 | -0.5654335 | 0.0063261 |
| Mitochondrial translation termination | -0.6604064 | -0.6820738 | -0.4651767 | 0.0644007 |
| Ribosomal scanning and start codon recognition | -0.5604403 | -0.7322144 | -0.4964662 | 0.1035661 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.5544242 | -0.7360135 | -0.4952892 | 0.0934073 |
| Translation initiation complex formation | -0.5512181 | -0.7315261 | -0.4969141 | 0.1005376 |
| Mitochondrial translation | -0.6410043 | -0.6716565 | -0.4664135 | 0.0619284 |
| APOBEC3G mediated resistance to HIV-1 infection | -0.4541784 | -0.5094298 | -0.7705920 | -0.1337638 |
| Selenoamino acid metabolism | -0.5591562 | -0.6956546 | -0.5290393 | 0.0234104 |
| YAP1- and WWTR1 (TAZ)-stimulated gene expression | 0.2499740 | 0.6402978 | 0.5627631 | 0.4595827 |
| Folding of actin by CCT/TriC | -0.5636182 | -0.5241621 | -0.5602710 | 0.3065533 |
| Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | -0.5284562 | -0.6620075 | -0.5282069 | 0.0414295 |
| Nonsense-Mediated Decay (NMD) | -0.5284562 | -0.6620075 | -0.5282069 | 0.0414295 |
| Regulation of expression of SLITs and ROBOs | -0.5355508 | -0.6597503 | -0.5008481 | 0.1047428 |
| Arachidonate production from DAG | -0.8173138 | -0.4495953 | 0.1968355 | -0.2642175 |
| Phosphate bond hydrolysis by NUDT proteins | -0.5383906 | -0.7730863 | -0.0518760 | 0.2935483 |
| Translation | -0.6010678 | -0.6188006 | -0.4696712 | 0.0594727 |
| LTC4-CYSLTR mediated IL4 production | 0.2796581 | -0.5652633 | -0.3885969 | -0.6465945 |
| Vpu mediated degradation of CD4 | -0.4668208 | -0.6472140 | -0.4826117 | 0.2852436 |
| RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) | 0.0383002 | 0.6761356 | 0.5626699 | 0.3958466 |
| Vif-mediated degradation of APOBEC3G | -0.5064613 | -0.6276994 | -0.4230027 | 0.3191459 |
| Complex III assembly | -0.6616507 | -0.6001844 | -0.3216473 | -0.0227284 |
| Classical antibody-mediated complement activation | -0.5772570 | 0.2385218 | 0.5385515 | -0.4676606 |
| Scavenging of heme from plasma | -0.5417744 | 0.2753666 | 0.5716097 | -0.4449542 |
| Regulation of activated PAK-2p34 by proteasome mediated degradation | -0.4719085 | -0.6079592 | -0.4271383 | 0.3355772 |
| Erythrocytes take up oxygen and release carbon dioxide | 0.3271060 | 0.5050408 | 0.3980668 | 0.6015304 |
| Cristae formation | -0.6654582 | -0.5625471 | -0.3297465 | 0.1157519 |
| Ubiquitin Mediated Degradation of Phosphorylated Cdc25A | -0.5150460 | -0.6186726 | -0.4132969 | 0.2479286 |
#mitch_report(res=mm2,outfile="multireactomestratified_eos_mitchreport.html",overwrite=TRUE)
l2 <- list("crp_pod1_a"=crp_pod1_a_adj, "crp pod1 b"=crp_pod1_b_adj,
"dex crplo pod1"=dex_crplo_pod1_adj, "dex crphi pod1"=dex_crphi_pod1_adj)
m2 <- mitch_import(x=l2, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mm2 <- mitch_calc(x=m2,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm2$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:7)]
rownames(top) <- top[,1]
top[,1] = NULL
colnames(top) <- gsub("^s\\.","",colnames(top))
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(7,20), cexRow=0.6, cexCol=0.7 )
as.matrix(top) |>
kbl(caption="Top REACTOMEs in multi enrichment analysis stratified POD1") |>
kable_paper("hover", full_width = F)| crp_pod1_a | crp.pod1.b | dex.crplo.pod1 | dex.crphi.pod1 | |
|---|---|---|---|---|
| MET activates PI3K/AKT signaling | 0.8254518 | -0.4128765 | -0.7084149 | 0.2996800 |
| Sulfide oxidation to sulfate | -0.6045934 | 0.2428840 | 0.7347515 | -0.5468562 |
| Establishment of Sister Chromatid Cohesion | 0.6803075 | -0.4141024 | -0.7731595 | -0.1288185 |
| CD163 mediating an anti-inflammatory response | 0.8177571 | 0.6035185 | 0.2169099 | 0.3802777 |
| Cohesin Loading onto Chromatin | 0.7608342 | -0.4192252 | -0.6719578 | 0.0913524 |
| Defects of platelet adhesion to exposed collagen | 0.0178692 | 0.6446714 | 0.7465995 | -0.4374735 |
| Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 0.7189407 | 0.5092484 | -0.4002134 | -0.4582765 |
| G2/M DNA replication checkpoint | 0.3610693 | 0.5359563 | -0.3615776 | -0.7507342 |
| Defective binding of VWF variant to GPIb:IX:V | 0.1990776 | 0.5923381 | 0.7482116 | -0.3911898 |
| Enhanced binding of GP1BA variant to VWF multimer:collagen | 0.1990776 | 0.5923381 | 0.7482116 | -0.3911898 |
| CD22 mediated BCR regulation | -0.3656458 | 0.5163140 | 0.1214210 | -0.8108435 |
| Erythrocytes take up oxygen and release carbon dioxide | 0.5903094 | 0.8004330 | -0.0565485 | -0.2809403 |
| Wax and plasmalogen biosynthesis | 0.5824548 | -0.6010730 | -0.5730422 | 0.1154367 |
| Phosphorylation of Emi1 | -0.1619523 | 0.6310224 | -0.0674762 | -0.7815849 |
| Scavenging of heme from plasma | -0.2928966 | 0.4724233 | 0.1116677 | -0.7763112 |
| NFE2L2 regulates pentose phosphate pathway genes | 0.7738997 | 0.4843728 | 0.2343728 | 0.1041068 |
| Activation of caspases through apoptosome-mediated cleavage | 0.3170801 | -0.5045104 | -0.6727695 | -0.2984578 |
| Classical antibody-mediated complement activation | -0.2974367 | 0.4468549 | 0.1245444 | -0.7520565 |
| Type I hemidesmosome assembly | 0.1200988 | 0.5509885 | 0.0846081 | -0.7227936 |
| ARMS-mediated activation | 0.5235249 | -0.3156838 | -0.6580066 | -0.1803078 |
| FCGR activation | -0.2533409 | 0.3941105 | 0.0183156 | -0.7704138 |
| Fructose metabolism | -0.4634956 | -0.3649090 | 0.6109385 | 0.2832130 |
| Creation of C4 and C2 activators | -0.2944315 | 0.4135374 | 0.1283458 | -0.7182992 |
| Biosynthesis of Lipoxins (LX) | 0.3713936 | 0.7323544 | 0.1977377 | -0.2653865 |
| Neurotransmitter clearance | 0.2082490 | 0.0614518 | 0.6183147 | 0.5651935 |
| Synthesis of PIPs at the late endosome membrane | 0.3813714 | -0.5026662 | -0.5609042 | 0.1883319 |
| Response to metal ions | 0.5292983 | 0.5816978 | -0.1615914 | -0.2810436 |
| Fructose catabolism | -0.4336408 | -0.2466867 | 0.6036333 | 0.3166792 |
| SMAC (DIABLO) binds to IAPs | 0.2033324 | -0.4876750 | -0.5429325 | -0.3549576 |
| SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes | 0.2033324 | -0.4876750 | -0.5429325 | -0.3549576 |
| SMAC, XIAP-regulated apoptotic response | 0.2033324 | -0.4876750 | -0.5429325 | -0.3549576 |
| SUMO is proteolytically processed | 0.1991967 | -0.5488147 | -0.5182692 | -0.2757880 |
| Scavenging by Class A Receptors | 0.6578355 | 0.1282587 | -0.2196865 | 0.4144801 |
| Common Pathway of Fibrin Clot Formation | 0.2776329 | 0.4569607 | 0.1834492 | -0.5753803 |
| Initial triggering of complement | -0.2787596 | 0.3783479 | 0.1346540 | -0.6400613 |
| Lysosphingolipid and LPA receptors | -0.4813448 | 0.3257954 | 0.3417500 | -0.4321370 |
| Unwinding of DNA | -0.3672928 | 0.2302230 | -0.0271566 | -0.6684164 |
| Mitotic Telophase/Cytokinesis | 0.5578734 | -0.1762567 | -0.5239751 | -0.1138273 |
| Regulation of IFNG signaling | 0.5575458 | -0.0247120 | -0.5526895 | 0.0014058 |
| Role of LAT2/NTAL/LAB on calcium mobilization | -0.2021757 | 0.3194979 | 0.0113667 | -0.6841033 |
| STAT5 activation downstream of FLT3 ITD mutants | 0.5945208 | 0.4826252 | -0.0123852 | 0.1456934 |
| MET activates RAP1 and RAC1 | 0.6576378 | -0.1930142 | -0.3387469 | 0.1342277 |
| Maturation of protein 3a_9683673 | 0.1829118 | 0.3807820 | -0.2558422 | -0.5931819 |
| Maturation of protein 3a_9694719 | 0.1829118 | 0.3807820 | -0.2558422 | -0.5931819 |
| Maturation of hRSV A proteins | 0.5255758 | -0.3835072 | -0.3965305 | 0.1109807 |
| OAS antiviral response | -0.1582725 | -0.3463168 | -0.5184396 | -0.4215933 |
| Protein repair | 0.4695408 | 0.1666431 | 0.0329458 | -0.5619460 |
| Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane | 0.2936302 | 0.5563925 | 0.2653830 | -0.3114888 |
| Transport of connexons to the plasma membrane | 0.2936302 | 0.5563925 | 0.2653830 | -0.3114888 |
| Butyrophilin (BTN) family interactions | -0.4953255 | -0.2848091 | 0.4091701 | 0.2623076 |
#mitch_report(res=mm2,outfile="multireactomestratified_pod1_mitchreport.html",overwrite=TRUE)Session information
For reproducibility
sessionInfo()## R version 4.5.3 (2026-03-11)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 LAPACK version 3.10.0
##
## locale:
## [1] C
##
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] gtools_3.9.5 xlsx_0.6.5
## [3] DT_0.34.0 eulerr_7.0.4
## [5] ggplot2_4.0.2 kableExtra_1.4.0
## [7] MASS_7.3-65 mitch_1.21.3
## [9] DESeq2_1.50.2 SummarizedExperiment_1.40.0
## [11] Biobase_2.70.0 MatrixGenerics_1.22.0
## [13] matrixStats_1.5.0 GenomicRanges_1.62.1
## [15] Seqinfo_1.0.0 IRanges_2.44.0
## [17] S4Vectors_0.48.0 BiocGenerics_0.56.0
## [19] generics_0.1.4 dplyr_1.2.0
## [21] WGCNA_1.73 fastcluster_1.3.0
## [23] dynamicTreeCut_1.63-1 reshape2_1.4.5
## [25] gplots_3.2.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_2.0.0
## [4] magrittr_2.0.4 farver_2.1.2 rmarkdown_2.30
## [7] vctrs_0.7.1 memoise_2.0.1.9000 base64enc_0.1-6
## [10] progress_1.2.3 htmltools_0.5.9 S4Arrays_1.10.1
## [13] SparseArray_1.10.8 Formula_1.2-5 sass_0.4.10
## [16] KernSmooth_2.23-26 bslib_0.10.0 htmlwidgets_1.6.4
## [19] plyr_1.8.9 echarts4r_0.4.6 impute_1.83.0
## [22] cachem_1.1.0 mime_0.13 lifecycle_1.0.5
## [25] iterators_1.0.14 pkgconfig_2.0.3 Matrix_1.7-5
## [28] R6_2.6.1 fastmap_1.2.0 shiny_1.13.0
## [31] digest_0.6.39 colorspace_2.1-2 GGally_2.4.0
## [34] AnnotationDbi_1.71.0 textshaping_1.0.4 Hmisc_5.2-4
## [37] RSQLite_2.4.4 labeling_0.4.3 polyclip_1.10-7
## [40] httr_1.4.7 abind_1.4-8 compiler_4.5.3
## [43] withr_3.0.2 bit64_4.6.0-1 doParallel_1.0.17
## [46] htmlTable_2.4.3 S7_0.2.1 backports_1.5.0
## [49] BiocParallel_1.44.0 DBI_1.2.3 ggstats_0.11.0
## [52] DelayedArray_0.36.0 caTools_1.18.3 tools_4.5.3
## [55] foreign_0.8-91 otel_0.2.0 beeswarm_0.4.0
## [58] httpuv_1.6.16 nnet_7.3-20 glue_1.8.0
## [61] promises_1.5.0 polylabelr_0.3.0 grid_4.5.3
## [64] checkmate_2.3.3 cluster_2.1.8.2 gtable_0.3.6
## [67] preprocessCore_1.71.0 tidyr_1.3.2 hms_1.1.4
## [70] data.table_1.18.2.1 xml2_1.5.0 XVector_0.50.0
## [73] foreach_1.5.2 pillar_1.11.1 stringr_1.6.0
## [76] later_1.4.8 rJava_1.0-18 splines_4.5.3
## [79] lattice_0.22-7 survival_3.8-6 bit_4.6.0
## [82] tidyselect_1.2.1 GO.db_3.21.0 locfit_1.5-9.12
## [85] Biostrings_2.77.1 knitr_1.51 gridExtra_2.3
## [88] svglite_2.2.2 xfun_0.56 stringi_1.8.7
## [91] UCSC.utils_1.5.0 statnet.common_4.12.0 yaml_2.3.12
## [94] xlsxjars_0.9.0 evaluate_1.0.5 codetools_0.2-20
## [97] tibble_3.3.1 cli_3.6.5 rpart_4.1.27
## [100] xtable_1.8-4 systemfonts_1.3.1 jquerylib_0.1.4
## [103] network_1.19.0 dichromat_2.0-0.1 Rcpp_1.1.1
## [106] GenomeInfoDb_1.45.4 coda_0.19-4.1 png_0.1-8
## [109] parallel_4.5.3 blob_1.2.4 prettyunits_1.2.0
## [112] bitops_1.0-9 viridisLite_0.4.3 scales_1.4.0
## [115] purrr_1.2.1 crayon_1.5.3 rlang_1.1.7
## [118] KEGGREST_1.49.0