PADDI enrichment analysis - Reactome
Mark Ziemann
2024-11-01
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
- avb_t0_adj
- avb_eos_adj
- avb_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.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 | 0.0059553 | -0.7101669 | 0.0428206 |
| 1492 | SUMO is proteolytically processed | 6 | 0.0058929 | -0.6491188 | 0.0425305 |
| 1141 | Phosphate bond hydrolysis by NUDT proteins | 7 | 0.0065798 | -0.5930633 | 0.0462745 |
| 979 | NOTCH4 Activation and Transmission of Signal to the Nucleus | 10 | 0.0012732 | -0.5883440 | 0.0145050 |
| 1361 | Regulation of NFE2L2 gene expression | 8 | 0.0042839 | 0.5831580 | 0.0342817 |
| 1633 | Small interfering RNA (siRNA) biogenesis | 9 | 0.0033815 | -0.5641147 | 0.0289609 |
| 155 | Beta-oxidation of pristanoyl-CoA | 9 | 0.0045002 | -0.5468033 | 0.0352517 |
| 317 | Cytochrome c-mediated apoptotic response | 13 | 0.0006671 | -0.5450005 | 0.0088792 |
| 1186 | Processing and activation of SUMO | 10 | 0.0036633 | -0.5306221 | 0.0303662 |
| 26 | ATF6 (ATF6-alpha) activates chaperones | 12 | 0.0020613 | -0.5136563 | 0.0202662 |
| 111 | Apoptosis induced DNA fragmentation | 10 | 0.0057719 | -0.5040897 | 0.0419695 |
| 558 | Formation of apoptosome | 11 | 0.0047614 | -0.4914847 | 0.0364093 |
| 1411 | Regulation of the apoptosome activity | 11 | 0.0047614 | -0.4914847 | 0.0364093 |
| 851 | MAPK3 (ERK1) activation | 10 | 0.0073218 | -0.4897347 | 0.0496801 |
| 87 | Advanced glycosylation endproduct receptor signaling | 12 | 0.0036717 | -0.4842926 | 0.0303662 |
| 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 | -0.4699681 | 0.0034007 |
| 104 | Antigen Presentation: Folding, assembly and peptide loading of class I MHC | 30 | 0.0000104 | -0.4649542 | 0.0003644 |
| 411 | Diseases of branched-chain amino acid catabolism | 13 | 0.0039261 | -0.4619362 | 0.0317879 |
| 989 | NRIF signals cell death from the nucleus | 15 | 0.0023776 | -0.4530863 | 0.0225696 |
| 217 | Calnexin/calreticulin cycle | 26 | 0.0000695 | -0.4506219 | 0.0015399 |
| 958 | N-glycan trimming in the ER and Calnexin/Calreticulin cycle | 35 | 0.0000052 | -0.4448415 | 0.0002190 |
| 730 | Incretin synthesis, secretion, and inactivation | 14 | 0.0045889 | -0.4375065 | 0.0355135 |
| 1692 | Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) | 14 | 0.0045889 | -0.4375065 | 0.0355135 |
| 1161 | Platelet sensitization by LDL | 16 | 0.0029602 | -0.4290862 | 0.0265318 |
| 715 | IRAK4 deficiency (TLR2/4) | 15 | 0.0050636 | -0.4179700 | 0.0381157 |
| 924 | Mitochondrial calcium ion transport | 22 | 0.0010350 | -0.4040187 | 0.0123882 |
| 1375 | Regulation of TLR by endogenous ligand | 15 | 0.0071834 | -0.4008633 | 0.0491033 |
| 661 | Golgi Associated Vesicle Biogenesis | 55 | 0.0000010 | -0.3805897 | 0.0000590 |
| 657 | Glycosphingolipid catabolism | 31 | 0.0004123 | -0.3664900 | 0.0061976 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDAn7eA/crp_t0_adj_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDAn7eA/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDAn7eA/rmarkdown-str383e3928c93c92.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- crp_eos_adj
myname <- "crp_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | -0.8425511 | 0.0000000 |
| 559 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.8424595 | 0.0000000 |
| 495 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.8344481 | 0.0000000 |
| 1867 | Viral mRNA Translation | 88 | 0.0000000 | -0.8310749 | 0.0000000 |
| 815 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.8264242 | 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 | -0.8220136 | 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 | -0.8166167 | 0.0000000 |
| 496 | Eukaryotic Translation Initiation | 118 | 0.0000000 | -0.8166167 | 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 | -0.8098811 | 0.0000000 |
| 934 | Mitochondrial translation initiation | 90 | 0.0000000 | -0.8069814 | 0.0000000 |
| 1487 | SRP-dependent cotranslational protein targeting to membrane | 111 | 0.0000000 | -0.8054049 | 0.0000000 |
| 1514 | Selenocysteine synthesis | 92 | 0.0000000 | -0.8045751 | 0.0000000 |
| 1039 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 94 | 0.0000000 | -0.8021991 | 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 | -0.7937154 | 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 | -0.7620725 | 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 | -0.7315676 | 0.0000000 |
| 1460 | SARS-CoV-2 modulates host translation machinery | 49 | 0.0000000 | -0.7302348 | 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/RtmpDAn7eA/crp_eos_adj_mitchreport.rds ".##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e39e3a9d7b.html##
## Output created: /tmp/RtmpDAn7eA/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.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 | 0.0359098 |
| 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 | 0.0448668 |
| 554 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.6857959 | 0.0000000 |
| 1120 | Peptide chain elongation | 88 | 0.0000000 | -0.6830681 | 0.0000000 |
| 490 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.6712218 | 0.0000000 |
| 1507 | Selenocysteine synthesis | 92 | 0.0000000 | -0.6661147 | 0.0000000 |
| 1856 | Viral mRNA Translation | 88 | 0.0000000 | -0.6576155 | 0.0000000 |
| 1447 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.6564731 | 0.0000000 |
| 444 | EGFR interacts with phospholipase C-gamma | 6 | 0.0054930 | 0.6545238 | 0.0363862 |
| 492 | Eukaryotic Translation Termination | 92 | 0.0000000 | -0.6545111 | 0.0000000 |
| 567 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | -0.6435482 | 0.0000000 |
| 809 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.6423205 | 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 | -0.6370369 | 0.0000000 |
| 1679 | Synthesis of diphthamide-EEF2 | 8 | 0.0018132 | -0.6367969 | 0.0159180 |
| 613 | GTP hydrolysis and joining of the 60S ribosomal subunit | 111 | 0.0000000 | -0.6301542 | 0.0000000 |
| 216 | Cap-dependent Translation Initiation | 118 | 0.0000000 | -0.6262694 | 0.0000000 |
| 491 | Eukaryotic Translation Initiation | 118 | 0.0000000 | -0.6262694 | 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 | -0.5977691 | 0.0000000 |
| 1793 | Translation initiation complex formation | 58 | 0.0000000 | -0.5923730 | 0.0000000 |
| 1356 | Regulation of NFE2L2 gene expression | 8 | 0.0038452 | 0.5901271 | 0.0287417 |
| 1483 | STAT5 activation downstream of FLT3 ITD mutants | 9 | 0.0021709 | 0.5901065 | 0.0181321 |
| 1426 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 100 | 0.0000000 | -0.5868331 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDAn7eA/crp_pod1_adj_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDAn7eA/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDAn7eA/rmarkdown-str383e397635871b.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEMulti-contrast enrichment analysis.
l1 <- list("crp_t0_adj"=crp_t0_adj,"crp_eos_adj"=crp_eos_adj,
"crp_pod1_adj"=crp_pod1_adj,"avb_t0_adj"=avb_t0_adj,
"avb_eos_adj"=avb_eos_adj,"avb_pod1_adj"=avb_pod1_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21771.6666666667## Note: no. genes in output = 21032## Note: estimated proportion of input genes in output = 0.966mm1 <- mitch_calc(x=m1,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$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.avb_t0_adj | s.avb_eos_adj | s.avb_pod1_adj | |
|---|---|---|---|---|---|---|
| Regulation of NFE2L2 gene expression | 0.5891124 | 0.6426941 | 0.5937738 | 0.8527516 | 0.1618389 | -0.0422493 |
| Protein repair | -0.5129839 | -0.4712578 | 0.3864580 | -0.4542788 | -0.7443958 | 0.6463743 |
| G2/M DNA replication checkpoint | -0.1564940 | -0.5453274 | 0.6956485 | 0.4163314 | -0.6025111 | 0.6742093 |
| Interleukin-21 signaling | 0.2427447 | 0.6305739 | 0.3235980 | 0.7074844 | 0.5108638 | 0.6565666 |
| Response to metal ions | 0.2238657 | -0.4391388 | 0.7772440 | 0.1266052 | -0.5004439 | 0.6562986 |
| Formation of xylulose-5-phosphate | -0.5645979 | -0.5993342 | -0.7188187 | 0.0256908 | 0.5512627 | -0.2090550 |
| MECP2 regulates transcription of neuronal ligands | 0.2891616 | 0.4716507 | -0.1094307 | 0.7554763 | 0.7264660 | 0.2340705 |
| CD163 mediating an anti-inflammatory response | -0.1675466 | 0.0306436 | 0.8753092 | -0.0382063 | -0.7842109 | -0.0578149 |
| Defective binding of VWF variant to GPIb:IX:V | 0.4129453 | -0.7073667 | 0.3276835 | -0.2818947 | -0.7251344 | 0.1212251 |
| Enhanced binding of GP1BA variant to VWF multimer:collagen | 0.4129453 | -0.7073667 | 0.3276835 | -0.2818947 | -0.7251344 | 0.1212251 |
| SUMO is conjugated to E1 (UBA2:SAE1) | -0.6691111 | -0.7382794 | -0.2371142 | -0.0034147 | -0.3656727 | 0.4093879 |
| Formation of a pool of free 40S subunits | -0.2566317 | -0.8482740 | -0.6834190 | -0.1132179 | -0.0326376 | -0.2669542 |
| Peptide chain elongation | -0.2300711 | -0.8496303 | -0.6805657 | -0.1098822 | -0.0032526 | -0.2731966 |
| Eukaryotic Translation Elongation | -0.2150399 | -0.8408237 | -0.6685987 | -0.1031363 | 0.0006468 | -0.2637795 |
| Tandem pore domain potassium channels | -0.2743235 | 0.4669710 | 0.3646455 | 0.4244923 | 0.6838921 | 0.4323489 |
| Viral mRNA Translation | -0.2357016 | -0.8380367 | -0.6547938 | -0.1133845 | -0.0177679 | -0.2422343 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.2894286 | -0.8311029 | -0.6395161 | -0.1316803 | -0.0702589 | -0.2270698 |
| MET activates PI3K/AKT signaling | -0.4461407 | 0.5910211 | 0.4899700 | -0.2374186 | -0.4362106 | 0.4578589 |
| Type I hemidesmosome assembly | 0.1838613 | 0.3568065 | 0.5685883 | 0.5944873 | 0.2748169 | 0.5740225 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.2881499 | -0.8265132 | -0.6271910 | -0.1367799 | -0.0694519 | -0.2223028 |
| Modulation by Mtb of host immune system | -0.4328656 | -0.8225786 | -0.3276847 | -0.1432376 | -0.4856735 | 0.0329200 |
| Selenocysteine synthesis | -0.2285296 | -0.8105845 | -0.6634018 | -0.0895205 | 0.0035070 | -0.2575310 |
| SARS-CoV-1 modulates host translation machinery | -0.1977731 | -0.8159914 | -0.6547094 | -0.1223513 | -0.0175113 | -0.2659501 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.2805386 | -0.8092074 | -0.6417244 | -0.1415258 | -0.0843798 | -0.2149835 |
| Cap-dependent Translation Initiation | -0.2791588 | -0.8205328 | -0.6233227 | -0.1298046 | -0.0611580 | -0.2299552 |
| Eukaryotic Translation Initiation | -0.2791588 | -0.8205328 | -0.6233227 | -0.1298046 | -0.0611580 | -0.2299552 |
| Phosphate bond hydrolysis by NUDT proteins | -0.5898896 | -0.7452421 | -0.4329879 | -0.2569798 | -0.2306030 | -0.0152947 |
| Eukaryotic Translation Termination | -0.2201376 | -0.8159864 | -0.6516199 | -0.0855008 | -0.0029801 | -0.2415845 |
| POLB-Dependent Long Patch Base Excision Repair | 0.1599957 | -0.2593584 | -0.5704790 | 0.6590088 | 0.5523568 | -0.1608638 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.2287798 | -0.8079049 | -0.6339680 | -0.0859481 | -0.0370451 | -0.2443447 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.3254653 | -0.7927068 | -0.5959163 | -0.1553078 | -0.1335494 | -0.2064002 |
| Translation initiation complex formation | -0.3192869 | -0.7895309 | -0.5904996 | -0.1471066 | -0.1325796 | -0.1938755 |
| Ribosomal scanning and start codon recognition | -0.3196355 | -0.7878260 | -0.5767469 | -0.1538259 | -0.1338620 | -0.1999372 |
| Fructose metabolism | -0.2746730 | -0.2257924 | -0.5791812 | -0.1399898 | 0.3878852 | -0.7030338 |
| SRP-dependent cotranslational protein targeting to membrane | -0.3137107 | -0.8098174 | -0.5609293 | -0.0984375 | -0.1043486 | -0.0969393 |
| RUNX1 regulates transcription of genes involved in BCR signaling | 0.0000793 | 0.3428929 | 0.5935667 | -0.1495609 | -0.6900029 | 0.3421954 |
| Replacement of protamines by nucleosomes in the male pronucleus | -0.2815335 | -0.6127894 | 0.2507770 | -0.2856882 | -0.6285363 | 0.3004757 |
| Activation of caspases through apoptosome-mediated cleavage | -0.5968166 | -0.2860427 | 0.1480389 | -0.0998446 | 0.0273629 | 0.7806208 |
| Phosphorylation of Emi1 | 0.2315229 | -0.2473287 | 0.4386315 | 0.7338533 | -0.0986239 | 0.4530898 |
| FASTK family proteins regulate processing and stability of mitochondrial RNAs | -0.0944954 | -0.7225076 | -0.0366615 | -0.1399710 | -0.6908079 | -0.1462528 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.2305147 | -0.7689840 | -0.5831897 | -0.1372638 | -0.0329512 | -0.2134849 |
| Post-transcriptional silencing by small RNAs | -0.2110888 | 0.7144488 | 0.3228877 | 0.2451979 | 0.3767148 | 0.4194530 |
| CD22 mediated BCR regulation | 0.1548736 | -0.5511716 | 0.2320515 | 0.4102152 | -0.5203513 | 0.4497008 |
| Mitochondrial translation initiation | -0.1122274 | -0.8032736 | -0.5660724 | 0.0899744 | -0.1013890 | -0.0876049 |
| Regulation of NPAS4 gene expression | -0.1496123 | 0.6113497 | 0.2834784 | 0.3270280 | 0.4091969 | 0.4966938 |
| SUMO is transferred from E1 to E2 (UBE2I, UBC9) | -0.4931748 | -0.6900696 | -0.3916358 | 0.0716630 | -0.2196093 | 0.2663156 |
| Formation of ATP by chemiosmotic coupling | -0.3101751 | -0.8499857 | -0.2985294 | 0.0290977 | -0.2920522 | 0.0350609 |
| Mitochondrial translation elongation | -0.1010272 | -0.7899935 | -0.5572109 | 0.0970002 | -0.1003470 | -0.1107609 |
| Activation of NIMA Kinases NEK9, NEK6, NEK7 | 0.0210837 | -0.0371870 | 0.4604111 | 0.4825616 | -0.1372991 | 0.7083336 |
| NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose | -0.0419366 | 0.1356637 | -0.0841109 | 0.6942217 | 0.4581823 | -0.4914729 |
mitch_report(res=mm1,outfile="multireactome_all_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpDAn7eA/multireactome_all_mitchreport.rds ".##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e39241f9c54.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEThis might work better if we work on each timepoint separately.
l1 <- list("crp_t0_adj"=crp_t0_adj, "avb_t0_adj"=avb_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.avb_t0_adj | |
|---|---|---|
| Regulation of NFE2L2 gene expression | 0.5831580 | 0.8540504 |
| MECP2 regulates transcription of neuronal ligands | 0.2836222 | 0.7573839 |
| Phosphorylation of Emi1 | 0.2254696 | 0.7360349 |
| NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | -0.0547762 | 0.7570586 |
| Interleukin-21 signaling | 0.2372210 | 0.7099553 |
| Loss of MECP2 binding ability to the NCoR/SMRT complex | 0.1218432 | 0.7078299 |
| Phosphate bond hydrolysis by NTPDase proteins | -0.7101669 | 0.0293528 |
| NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose | -0.0498605 | 0.6971964 |
| POLB-Dependent Long Patch Base Excision Repair | 0.1545604 | 0.6626338 |
| SUMO is proteolytically processed | -0.6491188 | 0.0691853 |
| Disorders of Developmental Biology | 0.1587519 | 0.6191555 |
| Disorders of Nervous System Development | 0.1587519 | 0.6191555 |
| Loss of function of MECP2 in Rett syndrome | 0.1587519 | 0.6191555 |
| Pervasive developmental disorders | 0.1587519 | 0.6191555 |
| Eicosanoids | 0.0688180 | -0.6353033 |
| Unwinding of DNA | 0.3670433 | 0.5219142 |
| Type I hemidesmosome assembly | 0.1770309 | 0.5976352 |
| NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | -0.1419701 | 0.5976580 |
| Repression of WNT target genes | 0.3720064 | 0.4706063 |
| NOTCH4 Activation and Transmission of Signal to the Nucleus | -0.5883440 | -0.0466880 |
| Small interfering RNA (siRNA) biogenesis | -0.5641147 | -0.1234009 |
| NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | -0.0718215 | 0.5723509 |
| Interleukin-2 signaling | 0.2021842 | 0.5265774 |
| Beta-oxidation of pristanoyl-CoA | -0.5468033 | -0.1304149 |
| TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest | 0.2702016 | 0.4912848 |
| Cytochrome c-mediated apoptotic response | -0.5450005 | -0.1277781 |
| Formation of annular gap junctions | -0.3688655 | 0.4207685 |
| Synthesis of pyrophosphates in the cytosol | -0.4556765 | 0.2980743 |
| Processing and activation of SUMO | -0.5306221 | 0.1210430 |
| Processive synthesis on the C-strand of the telomere | 0.0634272 | 0.5353507 |
| TGFBR3 regulates TGF-beta signaling | -0.2281356 | 0.4854771 |
| Glycosphingolipid transport | -0.4073092 | 0.3441104 |
| Removal of the Flap Intermediate from the C-strand | -0.0132786 | 0.5311453 |
| Cohesin Loading onto Chromatin | -0.4495151 | 0.2808966 |
| NR1H2 and NR1H3-mediated signaling | -0.1034382 | 0.5173912 |
| ATF6 (ATF6-alpha) activates chaperones | -0.5136563 | 0.0868866 |
| Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy | -0.4836414 | -0.1770328 |
| Miscellaneous substrates | 0.4991195 | -0.1047937 |
| SARS-CoV-2 modulates autophagy | -0.3592571 | 0.3609372 |
| Antigen Presentation: Folding, assembly and peptide loading of class I MHC | -0.4649542 | 0.2040720 |
| Response of EIF2AK1 (HRI) to heme deficiency | -0.2431696 | -0.4425591 |
| Advanced glycosylation endproduct receptor signaling | -0.4842926 | -0.1356635 |
| HDMs demethylate histones | 0.0890679 | 0.4926871 |
| MAPK3 (ERK1) activation | -0.4897347 | 0.0997896 |
| TGFBR3 PTM regulation | -0.4738975 | 0.1511528 |
| Fatty acids | 0.3749085 | -0.3264226 |
| MASTL Facilitates Mitotic Progression | -0.4835590 | 0.0666423 |
| ATF6 (ATF6-alpha) activates chaperone genes | -0.4699085 | 0.1211802 |
| Establishment of Sister Chromatid Cohesion | -0.4163669 | 0.2386743 |
| HSF1-dependent transactivation | 0.2537515 | 0.4033791 |
mitch_report(res=mm1,outfile="multireactome_t0_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpDAn7eA/multireactome_t0_mitchreport.rds ".##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e3962196fd3.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEl1 <- list("crp_eos_adj"=crp_eos_adj, "avb_eos_adj"=avb_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.avb_eos_adj | |
|---|---|---|
| FASTK family proteins regulate processing and stability of mitochondrial RNAs | -0.7269910 | -0.6869882 |
| Formation of the ureteric bud | -0.4916795 | -0.8236064 |
| Modulation by Mtb of host immune system | -0.8262745 | -0.4783947 |
| Mitochondrial RNA degradation | -0.6840302 | -0.6015691 |
| Defective binding of VWF variant to GPIb:IX:V | -0.5438601 | -0.7242894 |
| Enhanced binding of GP1BA variant to VWF multimer:collagen | -0.5438601 | -0.7242894 |
| Formation of ATP by chemiosmotic coupling | -0.8530097 | -0.2819965 |
| Protein repair | -0.4770912 | -0.7398566 |
| MECP2 regulates transcription of neuronal ligands | 0.4675457 | 0.7330181 |
| tRNA processing in the mitochondrion | -0.6357072 | -0.5660940 |
| RNA Polymerase I Promoter Opening | -0.6758658 | -0.5063100 |
| Peptide chain elongation | -0.8425511 | 0.0139946 |
| Formation of a pool of free 40S subunits | -0.8424595 | -0.0159496 |
| Eukaryotic Translation Elongation | -0.8344481 | 0.0176217 |
| Viral mRNA Translation | -0.8310749 | -0.0004979 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.8264242 | -0.0539657 |
| SUMO is conjugated to E1 (UBA2:SAE1) | -0.7435119 | -0.3562608 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.8220136 | -0.0532062 |
| Formation of xylulose-5-phosphate | -0.6024007 | 0.5604438 |
| SARS-CoV-1 modulates host translation machinery | -0.8190467 | -0.0051602 |
| Cap-dependent Translation Initiation | -0.8166167 | -0.0453540 |
| Eukaryotic Translation Initiation | -0.8166167 | -0.0453540 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.8125909 | -0.0726780 |
| Interleukin-21 signaling | 0.6277601 | 0.5174271 |
| Mitochondrial translation initiation | -0.8069814 | -0.0908860 |
| rRNA processing in the mitochondrion | -0.6804437 | -0.4416951 |
| SRP-dependent cotranslational protein targeting to membrane | -0.8054049 | -0.0880848 |
| Eukaryotic Translation Termination | -0.8098811 | 0.0138242 |
| Post-transcriptional silencing by small RNAs | 0.7119602 | 0.3857117 |
| Packaging Of Telomere Ends | -0.6982394 | -0.4097680 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.7962023 | -0.1222935 |
| Selenocysteine synthesis | -0.8045751 | 0.0205225 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.8021991 | -0.0201674 |
| Translation initiation complex formation | -0.7930814 | -0.1213222 |
| Ribosomal scanning and start codon recognition | -0.7914203 | -0.1226267 |
| Mitochondrial translation elongation | -0.7937154 | -0.0899042 |
| Mitochondrial translation termination | -0.7834619 | -0.0900117 |
| Phosphate bond hydrolysis by NUDT proteins | -0.7494543 | -0.2234319 |
| Mitochondrial translation | -0.7762521 | -0.0838498 |
| Regulation of CDH11 mRNA translation by microRNAs | 0.6300191 | 0.4580055 |
| Regulation of NPAS4 mRNA translation | 0.6300191 | 0.4580055 |
| Replacement of protamines by nucleosomes in the male pronucleus | -0.5182949 | -0.5802574 |
| Complex III assembly | -0.7620725 | -0.0632469 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.7641189 | -0.0164665 |
| RUNX1 regulates transcription of genes involved in BCR signaling | 0.3380166 | -0.6845663 |
| Arachidonate production from DAG | -0.7412203 | -0.1408020 |
| CD163 mediating an anti-inflammatory response | 0.0320449 | -0.7518569 |
| Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 | -0.5815028 | -0.4711611 |
| CD22 mediated BCR regulation | -0.5349739 | -0.5128959 |
| Regulation of NPAS4 gene expression | 0.6083070 | 0.4176658 |
mitch_report(res=mm1,outfile="multireactome_eos_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpDAn7eA/multireactome_eos_mitchreport.rds ".##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e3911f2d1b7.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEl1 <- list("crp_pod1_adj"=crp_pod1_adj, "avb_pod1_adj"=avb_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.avb_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 | 0.6563593 |
| G2/M DNA replication checkpoint | 0.6916039 | 0.6744917 |
| Fructose metabolism | -0.5808825 | -0.7031643 |
| CD163 mediating an anti-inflammatory response | 0.8726171 | -0.0579077 |
| Butyrophilin (BTN) family interactions | -0.5751165 | -0.6249212 |
| Activation of NIMA Kinases NEK9, NEK6, NEK7 | 0.4563548 | 0.7084224 |
| Regulation of IFNA/IFNB signaling | 0.4407278 | 0.6790170 |
| Type I hemidesmosome assembly | 0.5655448 | 0.5740998 |
| Activation of caspases through apoptosome-mediated cleavage | 0.1436752 | 0.7807220 |
| 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 | 0.3437615 | 0.6894745 |
| Maturation of protein 3a_9683673 | 0.4537124 | 0.6123873 |
| Maturation of protein 3a_9694719 | 0.4537124 | 0.6123873 |
| Neurotransmitter clearance | -0.1916663 | -0.7300011 |
| Synthesis of diphthamide-EEF2 | -0.6367969 | -0.3932337 |
| NFE2L2 regulates pentose phosphate pathway genes | 0.7010826 | 0.2181690 |
| Formation of a pool of free 40S subunits | -0.6857959 | -0.2577677 |
| Peptide chain elongation | -0.6830681 | -0.2626871 |
| Interleukin-21 signaling | 0.3206029 | 0.6566665 |
| Mitotic Telophase/Cytokinesis | 0.4479647 | 0.5647182 |
| Eukaryotic Translation Elongation | -0.6712218 | -0.2539332 |
| Selenocysteine synthesis | -0.6661147 | -0.2476521 |
| SARS-CoV-1 modulates host translation machinery | -0.6564731 | -0.2660393 |
| Viral mRNA Translation | -0.6576155 | -0.2320673 |
| Eukaryotic Translation Termination | -0.6545111 | -0.2318704 |
| EGFR interacts with phospholipase C-gamma | 0.6545238 | -0.2238120 |
| Platelet sensitization by LDL | 0.4364788 | 0.5273697 |
| Interleukin-6 signaling | 0.3321000 | 0.5967330 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.6370369 | -0.2348048 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.6423205 | -0.2190744 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.6435482 | -0.2150500 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.6301542 | -0.2144223 |
| Cap-dependent Translation Initiation | -0.6262694 | -0.2224674 |
| Eukaryotic Translation Initiation | -0.6262694 | -0.2224674 |
| Cohesin Loading onto Chromatin | 0.3900391 | 0.5317705 |
| N-Glycan antennae elongation | 0.4727885 | 0.4595201 |
| SMAC (DIABLO) binds to IAPs | 0.0041151 | 0.6410081 |
| SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes | 0.0041151 | 0.6410081 |
| SMAC, XIAP-regulated apoptotic response | 0.0041151 | 0.6410081 |
| Common Pathway of Fibrin Clot Formation | 0.4487614 | 0.4555628 |
| rRNA modification in the mitochondrion | -0.6392092 | 0.0022123 |
| Regulation of TP53 Activity through Association with Co-factors | -0.2347921 | -0.5929163 |
| Condensation of Prometaphase Chromosomes | 0.2865763 | 0.5655434 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.5977691 | -0.2064575 |
| Translation initiation complex formation | -0.5923730 | -0.1939364 |
| Regulation of IFNG signaling | 0.3808694 | 0.4926046 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.5868331 | -0.2048126 |
| Interaction between L1 and Ankyrins | 0.4903407 | 0.3804154 |
mitch_report(res=mm1,outfile="multireactome_eos_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDAn7eA/multireactome_eos_mitchreport.rds ".##
##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e39778898ae.html##
## Output created: /tmp/RtmpDAn7eA/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
- avb_crplo_t0_adj
- avb_crphi_t0_adj
- avb_crplo_eos_adj
- avb_crphi_eos_adj
- avb_crplo_pod1_adj
- avb_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 | 0.0001742 | -0.8191726 | 0.0009458 |
| 1125 | Peptide chain elongation | 87 | 0.0000000 | -0.8159484 | 0.0000000 |
| 879 | Maturation of spike protein_9683686 | 5 | 0.0017668 | -0.8074000 | 0.0071527 |
| 1862 | Viral mRNA Translation | 87 | 0.0000000 | -0.8061665 | 0.0000000 |
| 547 | Formation of ATP by chemiosmotic coupling | 20 | 0.0000000 | -0.7990618 | 0.0000000 |
| 492 | Eukaryotic Translation Elongation | 92 | 0.0000000 | -0.7971197 | 0.0000000 |
| 556 | Formation of a pool of free 40S subunits | 99 | 0.0000000 | -0.7868557 | 0.0000000 |
| 1452 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.7859480 | 0.0000000 |
| 494 | Eukaryotic Translation Termination | 91 | 0.0000000 | -0.7823269 | 0.0000000 |
| 659 | Glycosphingolipid transport | 7 | 0.0004072 | -0.7715383 | 0.0020381 |
| 1512 | Selenocysteine synthesis | 91 | 0.0000000 | -0.7670394 | 0.0000000 |
| 1037 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 93 | 0.0000000 | -0.7653626 | 0.0000000 |
| 1647 | Sulfide oxidation to sulfate | 5 | 0.0032844 | -0.7591036 | 0.0120784 |
| 1485 | SRP-dependent cotranslational protein targeting to membrane | 110 | 0.0000000 | -0.7565149 | 0.0000000 |
| 812 | L13a-mediated translational silencing of Ceruloplasmin expression | 109 | 0.0000000 | -0.7511498 | 0.0000000 |
| 557 | Formation of annular gap junctions | 10 | 0.0000428 | -0.7470906 | 0.0002572 |
| 616 | GTP hydrolysis and joining of the 60S ribosomal subunit | 110 | 0.0000000 | -0.7368549 | 0.0000000 |
| 150 | Beta oxidation of hexanoyl-CoA to butanoyl-CoA | 5 | 0.0048371 | -0.7275829 | 0.0163527 |
| 1141 | Phosphate bond hydrolysis by NUDT proteins | 7 | 0.0009239 | -0.7229631 | 0.0040834 |
| 218 | Cap-dependent Translation Initiation | 117 | 0.0000000 | -0.7219937 | 0.0000000 |
| 493 | Eukaryotic Translation Initiation | 117 | 0.0000000 | -0.7219937 | 0.0000000 |
| 1431 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 99 | 0.0000000 | -0.7211841 | 0.0000000 |
| 569 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | -0.7012210 | 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 | -0.6711538 | 0.0000000 |
| 1491 | SUMO is conjugated to E1 (UBA2:SAE1) | 5 | 0.0095950 | -0.6688223 | 0.0286217 |
| 577 | Fructose metabolism | 7 | 0.0022264 | -0.6674355 | 0.0087917 |
| 1511 | Selenoamino acid metabolism | 114 | 0.0000000 | -0.6654611 | 0.0000000 |
| 1185 | Prevention of phagosomal-lysosomal fusion | 9 | 0.0005887 | -0.6614875 | 0.0027806 |
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/RtmpDAn7eA/crp_t0_a_adj_mitchreport.rds ".##
##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e391cfc1845.html##
## Output created: /tmp/RtmpDAn7eA/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 | 0.0003484 | -0.6226643 | 0.0318253 |
| 1674 | Synthesis of PIPs at the early endosome membrane | 16 | 0.0000300 | -0.6025670 | 0.0082683 |
| 1625 | Signaling by cytosolic FGFR1 fusion mutants | 18 | 0.0006981 | -0.4615189 | 0.0343955 |
| 724 | Impaired BRCA2 binding to PALB2 | 24 | 0.0002602 | -0.4305937 | 0.0294892 |
| 511 | FGFR1 mutant receptor activation | 25 | 0.0007140 | -0.3909636 | 0.0343955 |
| 359 | Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function | 25 | 0.0008240 | -0.3863969 | 0.0345167 |
| 360 | Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function | 25 | 0.0008240 | -0.3863969 | 0.0345167 |
| 369 | Defective homologous recombination repair (HRR) due to BRCA1 loss of function | 25 | 0.0008240 | -0.3863969 | 0.0345167 |
| 371 | Defective homologous recombination repair (HRR) due to PALB2 loss of function | 25 | 0.0008240 | -0.3863969 | 0.0345167 |
| 1560 | Signaling by FGFR1 in disease | 32 | 0.0001903 | -0.3810903 | 0.0271628 |
| 1818 | Transport of Ribonucleoproteins into the Host Nucleus | 32 | 0.0013713 | -0.3268815 | 0.0489361 |
| 725 | Impaired BRCA2 binding to RAD51 | 35 | 0.0011148 | -0.3183604 | 0.0421228 |
| 1184 | Presynaptic phase of homologous DNA pairing and strand exchange | 40 | 0.0005816 | -0.3142945 | 0.0343955 |
| 180 | CD22 mediated BCR regulation | 59 | 0.0000360 | 0.3109448 | 0.0082683 |
| 370 | Defective homologous recombination repair (HRR) due to BRCA2 loss of function | 41 | 0.0006273 | -0.3085949 | 0.0343955 |
| 407 | Diseases of DNA Double-Strand Break Repair | 41 | 0.0006273 | -0.3085949 | 0.0343955 |
| 990 | NS1 Mediated Effects on Host Pathways | 40 | 0.0007562 | -0.3077462 | 0.0345167 |
| 1676 | Synthesis of PIPs at the plasma membrane | 52 | 0.0002070 | -0.2973903 | 0.0271628 |
| 700 | Homologous DNA Pairing and Strand Exchange | 43 | 0.0007509 | -0.2970068 | 0.0345167 |
| 720 | ISG15 antiviral mechanism | 72 | 0.0000229 | -0.2885535 | 0.0082683 |
| 1508 | Scavenging of heme from plasma | 71 | 0.0000475 | 0.2791206 | 0.0083229 |
| 661 | Golgi Associated Vesicle Biogenesis | 55 | 0.0004045 | -0.2756860 | 0.0324818 |
| 408 | Diseases of DNA repair | 51 | 0.0013386 | -0.2596037 | 0.0486702 |
| 273 | Classical antibody-mediated complement activation | 70 | 0.0004721 | 0.2416199 | 0.0343955 |
| 742 | Initial triggering of complement | 80 | 0.0002446 | 0.2371696 | 0.0294596 |
| 307 | Creation of C4 and C2 activators | 72 | 0.0006709 | 0.2317873 | 0.0343955 |
| 598 | G2/M DNA damage checkpoint | 66 | 0.0012625 | -0.2294783 | 0.0467855 |
| 1381 | Regulation of TP53 Activity through Phosphorylation | 88 | 0.0003955 | -0.2184821 | 0.0324818 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDAn7eA/crp_t0_b_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDAn7eA/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDAn7eA/rmarkdown-str383e397b92e927.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- crp_eos_a_adj
myname <- "crp_eos_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | 0.0015506 | -0.8172593 | 0.0107758 |
| 550 | Formation of ATP by chemiosmotic coupling | 20 | 0.0000000 | -0.8137176 | 0.0000000 |
| 860 | MET activates PI3K/AKT signaling | 5 | 0.0026253 | 0.7768482 | 0.0169034 |
| 1093 | PI3K events in ERBB4 signaling | 6 | 0.0015331 | 0.7468437 | 0.0106932 |
| 873 | Malate-aspartate shuttle | 8 | 0.0004347 | -0.7181915 | 0.0036836 |
| 1014 | Negative regulation of activity of TFAP2 (AP-2) family transcription factors | 6 | 0.0023569 | -0.7168645 | 0.0153837 |
| 1669 | Synthesis of Ketone Bodies | 6 | 0.0027733 | -0.7052395 | 0.0176253 |
| 1213 | Purine ribonucleoside monophosphate biosynthesis | 9 | 0.0003046 | -0.6950836 | 0.0026722 |
| 882 | Maturation of spike protein_9683686 | 5 | 0.0071625 | -0.6944076 | 0.0385460 |
| 811 | Ketone body metabolism | 8 | 0.0007271 | -0.6898390 | 0.0057811 |
| 933 | Mitochondrial translation elongation | 90 | 0.0000000 | -0.6894478 | 0.0000000 |
| 1127 | Peptide chain elongation | 88 | 0.0000000 | -0.6817362 | 0.0000000 |
| 934 | Mitochondrial translation initiation | 90 | 0.0000000 | -0.6774527 | 0.0000000 |
| 1867 | Viral mRNA Translation | 88 | 0.0000000 | -0.6690817 | 0.0000000 |
| 310 | Cristae formation | 33 | 0.0000000 | -0.6654306 | 0.0000000 |
| 495 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.6644667 | 0.0000000 |
| 291 | Complex III assembly | 23 | 0.0000000 | -0.6616111 | 0.0000009 |
| 935 | Mitochondrial translation termination | 90 | 0.0000000 | -0.6603892 | 0.0000000 |
| 497 | Eukaryotic Translation Termination | 92 | 0.0000000 | -0.6569322 | 0.0000000 |
| 1487 | SRP-dependent cotranslational protein targeting to membrane | 111 | 0.0000000 | -0.6547592 | 0.0000000 |
| 559 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.6511485 | 0.0000000 |
| 1514 | Selenocysteine synthesis | 92 | 0.0000000 | -0.6490937 | 0.0000000 |
| 1454 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.6478269 | 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 | -0.6441316 | 0.0000000 |
| 932 | Mitochondrial translation | 96 | 0.0000000 | -0.6409900 | 0.0000000 |
| 930 | Mitochondrial protein import | 63 | 0.0000000 | -0.6386993 | 0.0000000 |
| 1055 | Nucleotide biosynthesis | 12 | 0.0001578 | -0.6298419 | 0.0014947 |
| 815 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.6233642 | 0.0000000 |
| 1415 | Release of apoptotic factors from the mitochondria | 6 | 0.0084755 | -0.6205611 | 0.0441514 |
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/RtmpDAn7eA/crp_eos_a_adj_mitchreport.rds ".##
##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e39ffbd777.html##
## Output created: /tmp/RtmpDAn7eA/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 | -0.8467717 | 0.0000000 |
| 559 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | -0.8436330 | 0.0000000 |
| 495 | Eukaryotic Translation Elongation | 93 | 0.0000000 | -0.8382738 | 0.0000000 |
| 1867 | Viral mRNA Translation | 88 | 0.0000000 | -0.8311226 | 0.0000000 |
| 1454 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | -0.8201015 | 0.0000000 |
| 1514 | Selenocysteine synthesis | 92 | 0.0000000 | -0.8080701 | 0.0000000 |
| 815 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | -0.8017651 | 0.0000000 |
| 220 | Cap-dependent Translation Initiation | 118 | 0.0000000 | -0.8002121 | 0.0000000 |
| 496 | Eukaryotic Translation Initiation | 118 | 0.0000000 | -0.8002121 | 0.0000000 |
| 619 | GTP hydrolysis and joining of the 60S ribosomal subunit | 111 | 0.0000000 | -0.7993759 | 0.0000000 |
| 497 | Eukaryotic Translation Termination | 92 | 0.0000000 | -0.7940374 | 0.0000000 |
| 572 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | -0.7819498 | 0.0000000 |
| 1143 | Phosphate bond hydrolysis by NUDT proteins | 7 | 0.0003960 | -0.7731383 | 0.0032699 |
| 1039 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 94 | 0.0000000 | -0.7669802 | 0.0000000 |
| 1433 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 100 | 0.0000000 | -0.7547760 | 0.0000000 |
| 1487 | SRP-dependent cotranslational protein targeting to membrane | 111 | 0.0000000 | -0.7528227 | 0.0000000 |
| 73 | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 59 | 0.0000000 | -0.7360382 | 0.0000000 |
| 360 | Defective GALNT3 causes HFTC | 9 | 0.0001379 | 0.7336769 | 0.0013254 |
| 1445 | Ribosomal scanning and start codon recognition | 58 | 0.0000000 | -0.7322396 | 0.0000000 |
| 1803 | Translation initiation complex formation | 58 | 0.0000000 | -0.7315512 | 0.0000000 |
| 1891 | Zygotic genome activation (ZGA) | 5 | 0.0048468 | 0.7274166 | 0.0269079 |
| 550 | Formation of ATP by chemiosmotic coupling | 20 | 0.0000000 | -0.7152782 | 0.0000005 |
| 1363 | Regulation of NFE2L2 gene expression | 8 | 0.0004992 | 0.7106657 | 0.0039527 |
| 934 | Mitochondrial translation initiation | 90 | 0.0000000 | -0.6965012 | 0.0000000 |
| 1513 | Selenoamino acid metabolism | 115 | 0.0000000 | -0.6956697 | 0.0000000 |
| 1304 | RUNX1 regulates transcription of genes involved in WNT signaling | 5 | 0.0072660 | 0.6931709 | 0.0364620 |
| 1460 | SARS-CoV-2 modulates host translation machinery | 49 | 0.0000000 | -0.6889368 | 0.0000000 |
| 1333 | Reelin signalling pathway | 5 | 0.0082385 | 0.6822588 | 0.0393979 |
| 935 | Mitochondrial translation termination | 90 | 0.0000000 | -0.6821002 | 0.0000000 |
| 933 | Mitochondrial translation elongation | 90 | 0.0000000 | -0.6802714 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDAn7eA/crp_eos_b_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDAn7eA/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDAn7eA/rmarkdown-str383e393a9c79c3.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- crp_pod1_a_adj
myname <- "crp_pod1_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | 0.0013901 | 0.8254330 | 0.0087839 |
| 178 | CD163 mediating an anti-inflammatory response | 8 | 0.0000618 | 0.8177689 | 0.0006978 |
| 962 | NFE2L2 regulates pentose phosphate pathway genes | 8 | 0.0001501 | 0.7738644 | 0.0013734 |
| 278 | Cohesin Loading onto Chromatin | 10 | 0.0000309 | 0.7608153 | 0.0004196 |
| 749 | Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 6 | 0.0022884 | 0.7189564 | 0.0132014 |
| 484 | Establishment of Sister Chromatid Cohesion | 11 | 0.0000933 | 0.6802732 | 0.0009435 |
| 1501 | Scavenging by Class A Receptors | 10 | 0.0003152 | 0.6578167 | 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 | 0.0069079 | 0.6367644 | 0.0320531 |
| 25 | ATF6 (ATF6-alpha) activates chaperone genes | 10 | 0.0007205 | 0.6175022 | 0.0049787 |
| 614 | Gain-of-function MRAS complexes activate RAF signaling | 8 | 0.0028705 | 0.6086373 | 0.0157549 |
| 1467 | SHOC2 M1731 mutant abolishes MRAS complex function | 8 | 0.0028705 | 0.6086373 | 0.0157549 |
| 1578 | Signaling by MRAS-complex mutants | 8 | 0.0028705 | 0.6086373 | 0.0157549 |
| 21 | APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway | 7 | 0.0053822 | -0.6074286 | 0.0259781 |
| 480 | Erythropoietin activates Phosphoinositide-3-kinase (PI3K) | 11 | 0.0006332 | 0.5949277 | 0.0044555 |
| 1483 | STAT5 activation downstream of FLT3 ITD mutants | 9 | 0.0020109 | 0.5944999 | 0.0120339 |
| 307 | Cross-presentation of particulate exogenous antigens (phagosomes) | 8 | 0.0037801 | 0.5912215 | 0.0195730 |
| 479 | Erythrocytes take up oxygen and release carbon dioxide | 7 | 0.0068365 | 0.5902960 | 0.0318508 |
| 1390 | Regulation of gene expression by Hypoxia-inducible Factor | 8 | 0.0045939 | 0.5786185 | 0.0226863 |
| 1563 | Signaling by FLT3 ITD and TKD mutants | 15 | 0.0001385 | 0.5682142 | 0.0012918 |
| 1156 | Platelet sensitization by LDL | 16 | 0.0000890 | 0.5657638 | 0.0009194 |
| 442 | EGFR Transactivation by Gastrin | 7 | 0.0097390 | 0.5641667 | 0.0419475 |
| 1299 | RUNX1 regulates transcription of genes involved in differentiation of keratinocytes | 7 | 0.0104171 | 0.5590834 | 0.0442727 |
| 939 | Mitotic Telophase/Cytokinesis | 13 | 0.0004956 | 0.5578661 | 0.0036066 |
| 1347 | Regulation of IFNG signaling | 14 | 0.0003032 | 0.5575592 | 0.0024998 |
| 1083 | PI-3K cascade:FGFR3 | 10 | 0.0030963 | 0.5401591 | 0.0166613 |
| 598 | GAB1 signalosome | 14 | 0.0005797 | 0.5310783 | 0.0041867 |
| 871 | Maturation of hRSV A proteins | 13 | 0.0010330 | 0.5255686 | 0.0068189 |
| 419 | Displacement of DNA glycosylase by APEX1 | 9 | 0.0064262 | -0.5245612 | 0.0304060 |
| 1066 | Organic cation transport | 8 | 0.0103850 | 0.5232055 | 0.0442343 |
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/RtmpDAn7eA/crp_pod1_a_adj_mitchreport.rds ".##
##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e391a251f5.html##
## Output created: /tmp/RtmpDAn7eA/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 | 0.0018914 | 0.7323387 | 0.0194295 |
| 1192 | Propionyl-CoA catabolism | 5 | 0.0052667 | -0.7205008 | 0.0432366 |
| 375 | Defects of platelet adhesion to exposed collagen | 6 | 0.0062418 | 0.6446714 | 0.0491411 |
| 356 | Defective GALNT3 causes HFTC | 8 | 0.0022063 | 0.6249000 | 0.0217352 |
| 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 | 0.0008452 | 0.5563768 | 0.0108493 |
| 1814 | Transport of connexons to the plasma membrane | 12 | 0.0008452 | 0.5563768 | 0.0108493 |
| 1181 | Processing and activation of SUMO | 10 | 0.0039181 | -0.5267712 | 0.0340023 |
| 180 | CD22 mediated BCR regulation | 58 | 0.0000000 | 0.5163059 | 0.0000000 |
| 408 | Diseases of branched-chain amino acid catabolism | 13 | 0.0013229 | -0.5142909 | 0.0148614 |
| 1413 | Repression of WNT target genes | 14 | 0.0008922 | 0.5128033 | 0.0112756 |
| 1670 | Synthesis of PIPs at the late endosome membrane | 11 | 0.0038886 | -0.5026834 | 0.0339543 |
| 1661 | Synthesis of Leukotrienes (LT) and Eoxins (EX) | 15 | 0.0009141 | 0.4944157 | 0.0113703 |
| 1503 | Scavenging of heme from plasma | 70 | 0.0000000 | 0.4724166 | 0.0000000 |
| 618 | Gap junction assembly | 16 | 0.0013965 | 0.4613587 | 0.0153513 |
| 283 | Common Pathway of Fibrin Clot Formation | 13 | 0.0043321 | 0.4569535 | 0.0365284 |
| 1149 | Plasma lipoprotein remodeling | 18 | 0.0008472 | 0.4542553 | 0.0108493 |
| 271 | Classical antibody-mediated complement activation | 69 | 0.0000000 | 0.4468467 | 0.0000000 |
| 55 | Activation of Matrix Metalloproteinases | 20 | 0.0006120 | 0.4424999 | 0.0086442 |
| 315 | Cytochrome c-mediated apoptotic response | 13 | 0.0059348 | -0.4406925 | 0.0469508 |
| 1799 | Translesion synthesis by POLI | 17 | 0.0022616 | -0.4277309 | 0.0220531 |
| 567 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000002 | -0.4208778 | 0.0000059 |
| 1800 | Translesion synthesis by POLK | 17 | 0.0026839 | -0.4204846 | 0.0252731 |
| 141 | BBSome-mediated cargo-targeting to cilium | 23 | 0.0005185 | -0.4180548 | 0.0075452 |
| 1793 | Translation initiation complex formation | 58 | 0.0000000 | -0.4172568 | 0.0000013 |
| 72 | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 59 | 0.0000000 | -0.4163219 | 0.0000011 |
| 159 | Binding and Uptake of Ligands by Scavenger Receptors | 90 | 0.0000000 | 0.4153244 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDAn7eA/crp_pod1_b_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDAn7eA/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDAn7eA/rmarkdown-str383e3928414f6.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- avb_crplo_t0_adj
myname <- "avb_crplo_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | 0.0002573 | -0.8615075 | 0.0043872 |
| 165 | Biosynthesis of Lipoxins (LX) | 6 | 0.0003343 | -0.8455452 | 0.0052468 |
| 163 | Biosynthesis of E-series 18(S)-resolvins | 5 | 0.0011737 | -0.8379511 | 0.0134622 |
| 1206 | Protein repair | 6 | 0.0009254 | -0.7807659 | 0.0114927 |
| 309 | Cross-presentation of particulate exogenous antigens (phagosomes) | 8 | 0.0002057 | -0.7577646 | 0.0036358 |
| 1658 | Synthesis of 15-eicosatetraenoic acid derivatives | 6 | 0.0027112 | -0.7068697 | 0.0240756 |
| 1659 | Synthesis of 5-eicosatetraenoic acids | 7 | 0.0015459 | -0.6909325 | 0.0164583 |
| 1657 | Synthesis of 12-eicosatetraenoic acid derivatives | 6 | 0.0050614 | -0.6607666 | 0.0399723 |
| 1105 | POLB-Dependent Long Patch Base Excision Repair | 8 | 0.0012662 | 0.6580825 | 0.0141184 |
| 1532 | Signal attenuation | 9 | 0.0006861 | -0.6534671 | 0.0090557 |
| 777 | Interleukin-21 signaling | 9 | 0.0011735 | 0.6246385 | 0.0134622 |
| 1062 | OAS antiviral response | 8 | 0.0025697 | 0.6155201 | 0.0231394 |
| 805 | Keratan sulfate degradation | 9 | 0.0031917 | -0.5675607 | 0.0274568 |
| 108 | Antimicrobial peptides | 34 | 0.0000000 | -0.5571722 | 0.0000014 |
| 1417 | Replacement of protamines by nucleosomes in the male pronucleus | 13 | 0.0005307 | -0.5549252 | 0.0074649 |
| 280 | Cohesin Loading onto Chromatin | 10 | 0.0026575 | 0.5487008 | 0.0238184 |
| 1266 | RNA Polymerase I Promoter Opening | 17 | 0.0000924 | -0.5476271 | 0.0022833 |
| 888 | Metabolism of Angiotensinogen to Angiotensins | 12 | 0.0010690 | -0.5453991 | 0.0127157 |
| 942 | Mitotic Telophase/Cytokinesis | 13 | 0.0009162 | 0.5309582 | 0.0114749 |
| 1430 | Response of EIF2AK1 (HRI) to heme deficiency | 14 | 0.0007096 | -0.5225763 | 0.0093019 |
| 987 | NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | 32 | 0.0000005 | 0.5125212 | 0.0000297 |
| 676 | HDR through MMEJ (alt-NHEJ) | 12 | 0.0024536 | 0.5049486 | 0.0223024 |
| 1703 | TGFBR3 expression | 20 | 0.0001030 | 0.5015286 | 0.0024802 |
| 285 | Common Pathway of Fibrin Clot Formation | 13 | 0.0017717 | -0.5006916 | 0.0182203 |
| 1362 | Regulation of NPAS4 gene expression | 11 | 0.0051223 | 0.4873923 | 0.0402882 |
| 42 | Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 | 20 | 0.0005120 | -0.4487117 | 0.0073279 |
| 1674 | Synthesis of PIPs at the early endosome membrane | 16 | 0.0021308 | 0.4434543 | 0.0204278 |
| 1292 | RORA activates gene expression | 18 | 0.0011448 | 0.4427360 | 0.0132888 |
| 1818 | Transport of Ribonucleoproteins into the Host Nucleus | 32 | 0.0000147 | 0.4424770 | 0.0005454 |
| 1666 | Synthesis of Leukotrienes (LT) and Eoxins (EX) | 16 | 0.0022628 | -0.4408575 | 0.0210576 |
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/RtmpDAn7eA/avb_crplo_t0_adj_mitchreport.rds ".##
##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e3993ef8cd.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- avb_crphi_t0_adj
myname <- "avb_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 | 0.0010265 | 0.7739054 | 0.0048071 |
| 273 | Classical antibody-mediated complement activation | 70 | 0.0000000 | 0.7615491 | 0.0000000 |
| 983 | NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose | 5 | 0.0038165 | 0.7470112 | 0.0146795 |
| 1508 | Scavenging of heme from plasma | 71 | 0.0000000 | 0.7387811 | 0.0000000 |
| 307 | Creation of C4 and C2 activators | 72 | 0.0000000 | 0.7354446 | 0.0000000 |
| 982 | NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | 8 | 0.0004602 | 0.7150993 | 0.0024363 |
| 879 | Maturation of spike protein_9683686 | 5 | 0.0057687 | 0.7128562 | 0.0204343 |
| 742 | Initial triggering of complement | 80 | 0.0000000 | 0.6920181 | 0.0000000 |
| 507 | FCGR activation | 77 | 0.0000000 | 0.6874476 | 0.0000000 |
| 1662 | Synthesis of GDP-mannose | 6 | 0.0038085 | 0.6820954 | 0.0146781 |
| 180 | CD22 mediated BCR regulation | 59 | 0.0000000 | 0.6782824 | 0.0000000 |
| 659 | Glycosphingolipid transport | 7 | 0.0020856 | 0.6716958 | 0.0089113 |
| 557 | Formation of annular gap junctions | 10 | 0.0002511 | 0.6685178 | 0.0014401 |
| 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 | 0.6455545 | 0.0000000 |
| 1647 | Sulfide oxidation to sulfate | 5 | 0.0125554 | 0.6445644 | 0.0385874 |
| 1837 | Type I hemidesmosome assembly | 8 | 0.0016043 | 0.6441199 | 0.0071395 |
| 406 | Diseases of Base Excision Repair | 5 | 0.0128519 | 0.6424240 | 0.0392482 |
| 984 | NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | 7 | 0.0034402 | 0.6384498 | 0.0135015 |
| 985 | NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake | 5 | 0.0137408 | 0.6362589 | 0.0411158 |
| 1845 | Unwinding of DNA | 12 | 0.0001961 | 0.6207720 | 0.0011699 |
| 660 | Glyoxylate metabolism and glycine degradation | 13 | 0.0001074 | 0.6203153 | 0.0007139 |
| 57 | Activation of NIMA Kinases NEK9, NEK6, NEK7 | 7 | 0.0045047 | 0.6199188 | 0.0168555 |
| 599 | G2/M DNA replication checkpoint | 5 | 0.0169823 | 0.6164098 | 0.0489893 |
| 1446 | Role of phospholipids in phagocytosis | 89 | 0.0000000 | 0.6104852 | 0.0000000 |
| 159 | Binding and Uptake of Ligands by Scavenger Receptors | 93 | 0.0000000 | 0.5990156 | 0.0000000 |
| 1361 | Regulation of NFE2L2 gene expression | 8 | 0.0036800 | 0.5929352 | 0.0142973 |
| 994 | Nef Mediated CD4 Down-regulation | 9 | 0.0021616 | 0.5903512 | 0.0091953 |
| 497 | Expression and translocation of olfactory receptors | 52 | 0.0000000 | -0.5868461 | 0.0000000 |
| 508 | FCGR3A-mediated IL10 synthesis | 100 | 0.0000000 | 0.5836040 | 0.0000000 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDAn7eA/avb_crphi_t0_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDAn7eA/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDAn7eA/rmarkdown-str383e3943954682.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- avb_crplo_eos_adj
myname <- "avb_crplo_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | 0.0012342 | -0.8342457 | 0.0111304 |
| 22 | APOBEC3G mediated resistance to HIV-1 infection | 5 | 0.0028352 | 0.7707920 | 0.0223579 |
| 180 | CD163 mediating an anti-inflammatory response | 9 | 0.0000762 | -0.7613764 | 0.0010301 |
| 573 | Formation of the ureteric bud | 5 | 0.0032974 | -0.7587888 | 0.0252798 |
| 1303 | RUNX1 regulates transcription of genes involved in BCR signaling | 6 | 0.0014637 | -0.7500114 | 0.0127960 |
| 1141 | Phenylalanine metabolism | 5 | 0.0043197 | 0.7369101 | 0.0301289 |
| 166 | Biosynthesis of Lipoxins (LX) | 6 | 0.0025317 | -0.7117719 | 0.0202121 |
| 1312 | RUNX3 regulates BCL2L11 (BIM) transcription | 5 | 0.0079601 | -0.6852596 | 0.0485137 |
| 1107 | POLB-Dependent Long Patch Base Excision Repair | 8 | 0.0009261 | 0.6761516 | 0.0086017 |
| 1127 | Peptide chain elongation | 88 | 0.0000000 | 0.6603553 | 0.0000000 |
| 495 | Eukaryotic Translation Elongation | 93 | 0.0000000 | 0.6530513 | 0.0000000 |
| 559 | Formation of a pool of free 40S subunits | 100 | 0.0000000 | 0.6442221 | 0.0000000 |
| 1454 | SARS-CoV-1 modulates host translation machinery | 36 | 0.0000000 | 0.6416928 | 0.0000000 |
| 497 | Eukaryotic Translation Termination | 92 | 0.0000000 | 0.6410548 | 0.0000000 |
| 1867 | Viral mRNA Translation | 88 | 0.0000000 | 0.6409421 | 0.0000000 |
| 1514 | Selenocysteine synthesis | 92 | 0.0000000 | 0.6339397 | 0.0000000 |
| 1039 | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 94 | 0.0000000 | 0.5898119 | 0.0000000 |
| 968 | NFE2L2 regulates pentose phosphate pathway genes | 8 | 0.0040551 | -0.5867059 | 0.0288031 |
| 619 | GTP hydrolysis and joining of the 60S ribosomal subunit | 111 | 0.0000000 | 0.5856885 | 0.0000000 |
| 1814 | Translocation of ZAP-70 to Immunological synapse | 24 | 0.0000007 | 0.5852408 | 0.0000162 |
| 815 | L13a-mediated translational silencing of Ceruloplasmin expression | 110 | 0.0000000 | 0.5844671 | 0.0000000 |
| 220 | Cap-dependent Translation Initiation | 118 | 0.0000000 | 0.5835718 | 0.0000000 |
| 496 | Eukaryotic Translation Initiation | 118 | 0.0000000 | 0.5835718 | 0.0000000 |
| 182 | CD22 mediated BCR regulation | 58 | 0.0000000 | -0.5790105 | 0.0000000 |
| 1433 | Response of EIF2AK4 (GCN2) to amino acid deficiency | 100 | 0.0000000 | 0.5730024 | 0.0000000 |
| 572 | Formation of the ternary complex, and subsequently, the 43S complex | 51 | 0.0000000 | 0.5727102 | 0.0000000 |
| 1510 | Scavenging of heme from plasma | 70 | 0.0000000 | -0.5710090 | 0.0000000 |
| 1460 | SARS-CoV-2 modulates host translation machinery | 49 | 0.0000000 | 0.5656083 | 0.0000000 |
| 1298 | RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) | 9 | 0.0034647 | -0.5626598 | 0.0260459 |
| 549 | Folding of actin by CCT/TriC | 10 | 0.0021468 | 0.5604439 | 0.0174270 |
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/RtmpDAn7eA/avb_crplo_eos_adj_mitchreport.rds ".##
##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e3975b0db1c.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- avb_crphi_eos_adj
myname <- "avb_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 | 0.0009984 | -0.7757468 | 0.0257181 |
| 180 | CD163 mediating an anti-inflammatory response | 9 | 0.0000712 | -0.7644889 | 0.0051406 |
| 580 | Fructose metabolism | 7 | 0.0018067 | 0.6809749 | 0.0371340 |
| 984 | NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | 8 | 0.0013045 | 0.6563367 | 0.0293055 |
| 862 | MET activates RAP1 and RAC1 | 10 | 0.0024962 | -0.5521670 | 0.0459306 |
| 25 | ATF6 (ATF6-alpha) activates chaperone genes | 10 | 0.0026500 | -0.5488562 | 0.0478489 |
| 309 | Creation of C4 and C2 activators | 71 | 0.0000000 | 0.4796170 | 0.0000000 |
| 745 | Initial triggering of complement | 79 | 0.0000000 | 0.4745091 | 0.0000000 |
| 1814 | Translocation of ZAP-70 to Immunological synapse | 24 | 0.0000615 | 0.4724308 | 0.0047518 |
| 275 | Classical antibody-mediated complement activation | 69 | 0.0000000 | 0.4698520 | 0.0000000 |
| 1510 | Scavenging of heme from plasma | 70 | 0.0000000 | 0.4471092 | 0.0000000 |
| 344 | DNA strand elongation | 32 | 0.0000948 | 0.3986434 | 0.0057422 |
| 182 | CD22 mediated BCR regulation | 58 | 0.0000002 | 0.3946163 | 0.0000443 |
| 1149 | Phosphorylation of CD3 and TCR zeta chains | 27 | 0.0006383 | 0.3796279 | 0.0199390 |
| 1082 | PD-1 signaling | 28 | 0.0006018 | 0.3745392 | 0.0197075 |
| 924 | Mitochondrial RNA degradation | 25 | 0.0012222 | -0.3735797 | 0.0287010 |
| 510 | FCGR activation | 76 | 0.0000000 | 0.3707618 | 0.0000073 |
| 693 | Hedgehog ligand biogenesis | 47 | 0.0000111 | -0.3704427 | 0.0011275 |
| 1065 | Olfactory Signaling Pathway | 61 | 0.0000006 | -0.3700399 | 0.0000923 |
| 500 | Expression and translocation of olfactory receptors | 56 | 0.0000018 | -0.3686971 | 0.0002204 |
| 989 | NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | 33 | 0.0002672 | 0.3665913 | 0.0117343 |
| 988 | NR1H2 and NR1H3-mediated signaling | 39 | 0.0001177 | 0.3562912 | 0.0063160 |
| 1448 | Role of phospholipids in phagocytosis | 88 | 0.0000000 | 0.3555053 | 0.0000031 |
| 700 | Hh mutants are degraded by ERAD | 42 | 0.0000817 | -0.3512276 | 0.0056404 |
| 699 | Hh mutants abrogate ligand secretion | 43 | 0.0000718 | -0.3498477 | 0.0051406 |
| 27 | AUF1 (hnRNP D0) binds and destabilizes mRNA | 42 | 0.0000904 | -0.3490741 | 0.0057422 |
| 1098 | PINK1-PRKN Mediated Mitophagy | 31 | 0.0008809 | -0.3451149 | 0.0238647 |
| 1387 | Regulation of activated PAK-2p34 by proteasome mediated degradation | 37 | 0.0004086 | -0.3357298 | 0.0153353 |
| 1447 | Role of LAT2/NTAL/LAB on calcium mobilization | 77 | 0.0000004 | 0.3356422 | 0.0000617 |
| 383 | Degradation of GLI1 by the proteasome | 46 | 0.0000951 | -0.3325325 | 0.0057422 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDAn7eA/avb_crphi_eos_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDAn7eA/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDAn7eA/rmarkdown-str383e3977a4c4f9.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- avb_crplo_pod1_adj
myname <- "avb_crplo_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=reactome,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | 0.7730825 | 0.0012307 |
| 278 | Cohesin Loading onto Chromatin | 10 | 0.0002337 | 0.6718637 | 0.0144840 |
| 11 | ALK mutants bind TKIs | 11 | 0.0008331 | 0.5817976 | 0.0355649 |
| 1670 | Synthesis of PIPs at the late endosome membrane | 11 | 0.0012769 | 0.5608357 | 0.0471709 |
| 1347 | Regulation of IFNG signaling | 14 | 0.0003429 | 0.5526222 | 0.0199592 |
| 939 | Mitotic Telophase/Cytokinesis | 13 | 0.0010722 | 0.5238809 | 0.0438247 |
| 1669 | Synthesis of PIPs at the early endosome membrane | 16 | 0.0007142 | 0.4885930 | 0.0333321 |
| 759 | Interferon alpha/beta signaling | 63 | 0.0000000 | 0.4160962 | 0.0000071 |
| 722 | Impaired BRCA2 binding to RAD51 | 35 | 0.0000868 | 0.3832945 | 0.0064121 |
| 1151 | Platelet Aggregation (Plug Formation) | 28 | 0.0011217 | -0.3556958 | 0.0447640 |
| 368 | Defective homologous recombination repair (HRR) due to BRCA2 loss of function | 41 | 0.0003855 | 0.3203548 | 0.0211601 |
| 404 | Diseases of DNA Double-Strand Break Repair | 41 | 0.0003855 | 0.3203548 | 0.0211601 |
| 674 | HDR through Single Strand Annealing (SSA) | 37 | 0.0008124 | 0.3180822 | 0.0354692 |
| 1179 | Presynaptic phase of homologous DNA pairing and strand exchange | 40 | 0.0005050 | 0.3177768 | 0.0255297 |
| 840 | M-decay: degradation of maternal mRNAs by maternally stored factors | 41 | 0.0011762 | 0.2928186 | 0.0447640 |
| 697 | Homologous DNA Pairing and Strand Exchange | 43 | 0.0011497 | 0.2865125 | 0.0447640 |
| 717 | ISG15 antiviral mechanism | 72 | 0.0000652 | 0.2721333 | 0.0050077 |
| 97 | Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal | 90 | 0.0000541 | 0.2461833 | 0.0047240 |
| 98 | Amplification of signal from the kinetochores | 90 | 0.0000541 | 0.2461833 | 0.0047240 |
| 1420 | Resolution of Sister Chromatid Cohesion | 115 | 0.0000117 | 0.2366289 | 0.0014921 |
| 938 | Mitotic Spindle Checkpoint | 107 | 0.0000395 | 0.2299801 | 0.0044589 |
| 1521 | Separation of Sister Chromatids | 167 | 0.0000086 | 0.1995432 | 0.0012307 |
| 231 | Cell Cycle Checkpoints | 245 | 0.0000001 | 0.1992893 | 0.0000365 |
| 109 | Antiviral mechanism by IFN-stimulated genes | 140 | 0.0000470 | 0.1992219 | 0.0047240 |
| 446 | EML4 and NUDC in mitotic spindle formation | 106 | 0.0005382 | 0.1945537 | 0.0265074 |
| 1421 | Respiratory Syncytial Virus Infection Pathway | 97 | 0.0009300 | 0.1945187 | 0.0388373 |
| 933 | Mitotic G1 phase and G1/S transition | 138 | 0.0001324 | 0.1884264 | 0.0094229 |
| 594 | G2/M Checkpoints | 126 | 0.0002898 | 0.1869480 | 0.0173977 |
| 935 | Mitotic Metaphase and Anaphase | 211 | 0.0000029 | 0.1868220 | 0.0006187 |
| 932 | Mitotic Anaphase | 210 | 0.0000033 | 0.1861449 | 0.0006377 |
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/RtmpDAn7eA/avb_crplo_pod1_adj_mitchreport.rds ".##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e393efe9abd.html##
## Output created: /tmp/RtmpDAn7eA/mitch_report.html## [1] TRUEde <- avb_crphi_pod1_adj
myname <- "avb_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 | 0.8133555 | 0.0000000 |
| 1143 | Phosphorylation of Emi1 | 6 | 0.0009131 | 0.7816476 | 0.0148651 |
| 1503 | Scavenging of heme from plasma | 70 | 0.0000000 | 0.7784045 | 0.0000000 |
| 505 | FCGR activation | 76 | 0.0000000 | 0.7723287 | 0.0000000 |
| 271 | Classical antibody-mediated complement activation | 69 | 0.0000000 | 0.7541541 | 0.0000000 |
| 596 | G2/M DNA replication checkpoint | 5 | 0.0036433 | 0.7507718 | 0.0426751 |
| 1831 | Type I hemidesmosome assembly | 8 | 0.0003990 | 0.7228289 | 0.0075881 |
| 305 | Creation of C4 and C2 activators | 71 | 0.0000000 | 0.7203392 | 0.0000000 |
| 1440 | Role of LAT2/NTAL/LAB on calcium mobilization | 77 | 0.0000000 | 0.6860033 | 0.0000000 |
| 1839 | Unwinding of DNA | 12 | 0.0000606 | 0.6684870 | 0.0015327 |
| 57 | Activation of NIMA Kinases NEK9, NEK6, NEK7 | 7 | 0.0023100 | 0.6650260 | 0.0301867 |
| 739 | Initial triggering of complement | 79 | 0.0000000 | 0.6419002 | 0.0000000 |
| 502 | FCERI mediated Ca+2 mobilization | 92 | 0.0000000 | 0.6270683 | 0.0000000 |
| 506 | FCGR3A-mediated IL10 synthesis | 99 | 0.0000000 | 0.6249791 | 0.0000000 |
| 105 | Antigen activates B Cell Receptor (BCR) leading to generation of second messengers | 83 | 0.0000000 | 0.6247918 | 0.0000000 |
| 1441 | Role of phospholipids in phagocytosis | 88 | 0.0000000 | 0.6236185 | 0.0000000 |
| 874 | Maturation of protein 3a_9683673 | 9 | 0.0020536 | 0.5932969 | 0.0279782 |
| 875 | Maturation of protein 3a_9694719 | 9 | 0.0020536 | 0.5932969 | 0.0279782 |
| 774 | Interleukin-21 signaling | 9 | 0.0020766 | 0.5926588 | 0.0280923 |
| 159 | Binding and Uptake of Ligands by Scavenger Receptors | 90 | 0.0000000 | 0.5911481 | 0.0000000 |
| 283 | Common Pathway of Fibrin Clot Formation | 13 | 0.0003266 | 0.5754962 | 0.0067469 |
| 503 | FCERI mediated MAPK activation | 93 | 0.0000000 | 0.5587292 | 0.0000000 |
| 507 | FCGR3A-mediated phagocytosis | 121 | 0.0000000 | 0.5548696 | 0.0000000 |
| 823 | Leishmania phagocytosis | 121 | 0.0000000 | 0.5548696 | 0.0000000 |
| 1114 | Parasite infection | 121 | 0.0000000 | 0.5548696 | 0.0000000 |
| 1379 | Regulation of actin dynamics for phagocytic cup formation | 123 | 0.0000000 | 0.5399367 | 0.0000000 |
| 592 | G1/S-Specific Transcription | 29 | 0.0000010 | 0.5250107 | 0.0000371 |
| 289 | Condensation of Prometaphase Chromosomes | 11 | 0.0026475 | 0.5233799 | 0.0330249 |
| 1338 | Regulation of Complement cascade | 96 | 0.0000000 | 0.5145726 | 0.0000000 |
| 103 | Anti-inflammatory response favouring Leishmania parasite infection | 131 | 0.0000000 | 0.5141371 | 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/RtmpDAn7eA/avb_crphi_pod1_adj_mitchreport.rds ".##
##
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## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e391874dbe6.html##
## Output created: /tmp/RtmpDAn7eA/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,
"avb crplo t0"=avb_crplo_t0_adj,
"avb crphi t0"=avb_crphi_t0_adj,
"avb crplo eos"=avb_crplo_eos_adj,
"avb crphi eos"=avb_crphi_eos_adj,
"avb crplo pod1"=avb_crplo_pod1_adj,
"avb crphi pod1"=avb_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 | avb.crplo.t0 | avb.crphi.t0 | avb.crplo.eos | avb.crphi.eos | avb.crplo.pod1 | avb.crphi.pod1 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sulfide oxidation to sulfate | -0.7545251 | 0.4949922 | -0.5282446 | -0.5489418 | -0.6024920 | 0.2471584 | -0.5506159 | 0.6384648 | 0.1763542 | 0.5081562 | -0.7342464 | 0.5458791 |
| CD163 mediating an anti-inflammatory response | -0.2419616 | 0.1677844 | 0.0896238 | 0.4070824 | 0.8194326 | 0.6062595 | -0.4284389 | 0.2133395 | -0.8105498 | -0.7893241 | -0.2168712 | -0.3812072 |
| Peptide chain elongation | -0.8125523 | 0.1859742 | -0.6870841 | -0.8502888 | -0.3449873 | -0.3654931 | -0.3635438 | 0.3761845 | 0.6538959 | -0.0018532 | -0.0460061 | -0.0140329 |
| Erythrocytes take up oxygen and release carbon dioxide | 0.4282317 | 0.5443791 | 0.3304026 | 0.5161542 | 0.5928249 | 0.8020588 | -0.4363717 | 0.4108646 | -0.4079701 | -0.6094989 | 0.0705215 | 0.2802038 |
| Biosynthesis of Lipoxins (LX) | -0.3777704 | 0.4643774 | -0.0179619 | 0.3309395 | 0.3733790 | 0.7351057 | -0.8469038 | 0.3733473 | -0.7176670 | -0.4231269 | -0.1980405 | 0.2641016 |
| CD22 mediated BCR regulation | -0.5434113 | 0.3039165 | -0.5276850 | 0.2817950 | -0.3728039 | 0.5136566 | -0.0557548 | 0.6858650 | -0.5819802 | 0.3906898 | -0.1298982 | 0.8099375 |
| Classical antibody-mediated complement activation | -0.6056489 | 0.2341269 | -0.5704162 | 0.2366045 | -0.3020065 | 0.4439796 | -0.0552572 | 0.7703290 | -0.5413720 | 0.4668956 | -0.1317679 | 0.7503143 |
| Scavenging of heme from plasma | -0.5647915 | 0.2727324 | -0.5343431 | 0.2744885 | -0.2974371 | 0.4701154 | -0.0973966 | 0.7463882 | -0.5742450 | 0.4438427 | -0.1181744 | 0.7749935 |
| Eukaryotic Translation Elongation | -0.7937285 | 0.1857574 | -0.6690679 | -0.8412244 | -0.3357086 | -0.3537696 | -0.3477908 | 0.3682094 | 0.6463457 | 0.0055614 | -0.0393235 | 0.0076398 |
| Viral mRNA Translation | -0.8025919 | 0.1654563 | -0.6742788 | -0.8344762 | -0.3144344 | -0.3588605 | -0.3512829 | 0.3616275 | 0.6343253 | -0.0195251 | -0.0192946 | -0.0189687 |
| Cohesin Loading onto Chromatin | 0.1659880 | -0.6739416 | 0.6198173 | 0.4809152 | 0.7625630 | -0.4167063 | 0.5489582 | 0.0163353 | -0.1694986 | -0.1615641 | 0.6714109 | -0.0929312 |
| Formation of a pool of free 40S subunits | -0.7830230 | 0.1421056 | -0.6549376 | -0.8462097 | -0.2844183 | -0.4003475 | -0.3383846 | 0.3544493 | 0.6370575 | -0.0320691 | -0.0164898 | -0.0377255 |
| SARS-CoV-1 modulates host translation machinery | -0.7824480 | 0.1985987 | -0.6437655 | -0.8170075 | -0.3477250 | -0.3338678 | -0.3548956 | 0.3464337 | 0.6332555 | -0.0455722 | -0.0400209 | 0.0037679 |
| Creation of C4 and C2 activators | -0.5878297 | 0.2243134 | -0.5406395 | 0.2121921 | -0.2987201 | 0.4103125 | -0.0550943 | 0.7429335 | -0.5134297 | 0.4767988 | -0.1354042 | 0.7160876 |
| Eukaryotic Translation Termination | -0.7785783 | 0.1620980 | -0.6615452 | -0.7964128 | -0.3190633 | -0.3653766 | -0.3105276 | 0.3567506 | 0.6344119 | -0.0174278 | -0.0155744 | -0.0106794 |
| Selenocysteine synthesis | -0.7633067 | 0.1564138 | -0.6536444 | -0.8105226 | -0.3218278 | -0.3698864 | -0.3083635 | 0.3558428 | 0.6270191 | -0.0030861 | -0.0162849 | -0.0208272 |
| Formation of ATP by chemiosmotic coupling | -0.7949933 | 0.0566629 | -0.8110080 | -0.7102370 | 0.1571816 | -0.2972587 | -0.4227632 | 0.5712498 | 0.2827051 | -0.1464496 | -0.0369884 | -0.0302970 |
| Phosphorylation of Emi1 | -0.3699864 | 0.1144298 | -0.3859507 | 0.3339992 | -0.1590095 | 0.6344684 | 0.3732680 | 0.7697454 | -0.2916072 | 0.4468436 | 0.0671550 | 0.7811915 |
| Fructose metabolism | -0.6619942 | 0.2944590 | -0.2563547 | -0.3798675 | -0.4615662 | -0.3622558 | -0.4717717 | 0.3366265 | 0.2657856 | 0.6766435 | -0.6105724 | -0.2846475 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.7614936 | 0.1435717 | -0.6483734 | -0.7688678 | -0.3021788 | -0.3551366 | -0.3015955 | 0.3495011 | 0.5824091 | -0.0354142 | -0.0162792 | -0.0230198 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.7470007 | 0.0927424 | -0.6260592 | -0.8031314 | -0.2256956 | -0.4060362 | -0.3343947 | 0.3319384 | 0.5763347 | -0.0547604 | 0.0162321 | -0.0420971 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.7325712 | 0.0838474 | -0.6227842 | -0.8006413 | -0.2132622 | -0.4033996 | -0.3256563 | 0.3164099 | 0.5775825 | -0.0610258 | 0.0223645 | -0.0436696 |
| Cap-dependent Translation Initiation | -0.7175225 | 0.0864047 | -0.6163045 | -0.8011798 | -0.2145277 | -0.3914170 | -0.3285071 | 0.3227729 | 0.5754072 | -0.0523826 | 0.0045602 | -0.0433325 |
| Eukaryotic Translation Initiation | -0.7175225 | 0.0864047 | -0.6163045 | -0.8011798 | -0.2145277 | -0.3914170 | -0.3285071 | 0.3227729 | 0.5754072 | -0.0523826 | 0.0045602 | -0.0433325 |
| FCGR activation | -0.5403490 | 0.2093907 | -0.4369907 | 0.3015565 | -0.2567740 | 0.3911215 | -0.0412101 | 0.6920717 | -0.4973594 | 0.3661523 | -0.0235027 | 0.7690064 |
| SRP-dependent cotranslational protein targeting to membrane | -0.7526006 | 0.0568831 | -0.6579772 | -0.7531359 | -0.1997124 | -0.3831860 | -0.3133761 | 0.3599265 | 0.5359022 | -0.0936882 | 0.0594051 | 0.0511536 |
| Fructose catabolism | -0.5632282 | 0.4345556 | -0.2395301 | -0.3512341 | -0.4317021 | -0.2436772 | -0.6638417 | 0.2040519 | 0.0864888 | 0.6086936 | -0.6035383 | -0.3180577 |
| Establishment of Sister Chromatid Cohesion | 0.1439297 | -0.6911833 | 0.3358762 | 0.3256268 | 0.6823955 | -0.4116273 | 0.4673638 | 0.0019591 | -0.2429129 | -0.0275612 | 0.7725046 | 0.1275218 |
| G2/M DNA replication checkpoint | -0.4509535 | -0.2228849 | -0.2255291 | 0.1675465 | 0.3647215 | 0.5400200 | 0.1402673 | 0.6120417 | -0.5925810 | 0.1351500 | 0.3612213 | 0.7501879 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.7169758 | 0.1514505 | -0.6232231 | -0.7559708 | -0.2502892 | -0.3327070 | -0.3474061 | 0.3133571 | 0.5651224 | -0.0240947 | -0.0155035 | -0.0097565 |
| NFE2L2 regulates pentose phosphate pathway genes | -0.3371623 | 0.2299753 | 0.4170591 | 0.4182125 | 0.7758514 | 0.4873716 | -0.2601907 | 0.4748740 | -0.5950937 | -0.3722888 | -0.2341253 | -0.1058076 |
| Initial triggering of complement | -0.5444270 | 0.2307191 | -0.5118452 | 0.1644628 | -0.2821137 | 0.3753338 | -0.0581261 | 0.6967766 | -0.4467185 | 0.4712043 | -0.1410464 | 0.6369275 |
| Protein repair | -0.6190431 | 0.0014902 | -0.1150639 | -0.1029360 | 0.4722566 | 0.1702812 | -0.7826183 | 0.2929389 | -0.5412822 | -0.4331621 | -0.0330385 | 0.5610514 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.6965340 | 0.0761557 | -0.5712984 | -0.7782027 | -0.1982288 | -0.4181084 | -0.3085116 | 0.2896692 | 0.5633958 | -0.0863293 | 0.0426203 | -0.0370802 |
| Defective binding of VWF variant to GPIb:IX:V | 0.2089219 | 0.2105959 | -0.2830932 | -0.4076949 | 0.2028345 | 0.5959481 | -0.3908403 | -0.0811433 | -0.5491321 | -0.4408903 | -0.7476007 | 0.3900984 |
| Enhanced binding of GP1BA variant to VWF multimer:collagen | 0.2089219 | 0.2105959 | -0.2830932 | -0.4076949 | 0.2028345 | 0.5959481 | -0.3908403 | -0.0811433 | -0.5491321 | -0.4408903 | -0.7476007 | 0.3900984 |
| Role of LAT2/NTAL/LAB on calcium mobilization | -0.5184522 | 0.1811163 | -0.3997725 | 0.2925604 | -0.2048503 | 0.3156991 | -0.0708766 | 0.6486247 | -0.5085831 | 0.3304781 | -0.0163526 | 0.6814466 |
| NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake | -0.6386931 | 0.0837495 | -0.2332715 | -0.3348552 | -0.0784420 | 0.2864222 | 0.2402530 | 0.6304561 | 0.3628953 | 0.2973986 | -0.6833214 | -0.3656727 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.6781431 | 0.0270331 | -0.5499298 | -0.7320704 | -0.1406805 | -0.4136287 | -0.3097954 | 0.2844763 | 0.4857909 | -0.1018315 | 0.0475308 | -0.0689046 |
| Modulation by Mtb of host immune system | -0.8150637 | -0.0349992 | -0.4537523 | -0.6214439 | 0.1229625 | -0.2785052 | -0.4999966 | 0.2807066 | -0.0020860 | -0.4610769 | 0.1456022 | 0.0266961 |
| Translation initiation complex formation | -0.6740348 | 0.0296574 | -0.5467229 | -0.7275149 | -0.1381333 | -0.4145740 | -0.3028216 | 0.2867195 | 0.4874853 | -0.1089510 | 0.0609835 | -0.0592392 |
| Ribosomal scanning and start codon recognition | -0.6662156 | 0.0269578 | -0.5559543 | -0.7282234 | -0.1250695 | -0.4083923 | -0.2988593 | 0.2753573 | 0.4870447 | -0.1120139 | 0.0600086 | -0.0702578 |
| Phosphate bond hydrolysis by NUDT proteins | -0.7169764 | -0.1221607 | -0.5332088 | -0.7682895 | -0.0642161 | -0.4847223 | -0.2694411 | 0.1545167 | 0.0441855 | -0.2997316 | 0.1990623 | -0.0517547 |
| NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | -0.5695158 | 0.1899853 | -0.2834618 | 0.0876617 | -0.0164574 | 0.3894359 | 0.2342323 | 0.7106521 | 0.3078387 | 0.6515649 | -0.3871290 | -0.0995291 |
| SARS-CoV-2 modulates host translation machinery | -0.6054688 | 0.1771220 | -0.5916850 | -0.6845104 | -0.2600793 | -0.2685663 | -0.2853068 | 0.2885319 | 0.5568094 | -0.0148974 | -0.0418580 | -0.0057821 |
| Selenoamino acid metabolism | -0.6608327 | 0.0921879 | -0.5610638 | -0.6952318 | -0.2299497 | -0.3152284 | -0.2570195 | 0.3057410 | 0.5209297 | -0.0335479 | 0.0072648 | -0.0511479 |
| Type I hemidesmosome assembly | -0.2404157 | 0.1954790 | -0.0031274 | 0.4687500 | 0.1227764 | 0.5536411 | 0.0888865 | 0.6382824 | 0.1166286 | 0.4762533 | -0.0843560 | 0.7222341 |
| Mitochondrial translation elongation | -0.5637825 | 0.0983202 | -0.6863284 | -0.6750464 | -0.1959847 | -0.3562209 | -0.1953289 | 0.3690659 | 0.4599370 | -0.0666136 | 0.0070640 | 0.0872282 |
| Synthesis of PIPs at the late endosome membrane | 0.3689514 | -0.6200682 | 0.3203593 | 0.2172849 | 0.3845375 | -0.5007849 | 0.3511424 | -0.3139934 | -0.4142308 | -0.0347488 | 0.5600763 | -0.1896588 |
| Mitochondrial translation initiation | -0.5407103 | 0.0718461 | -0.6742240 | -0.6913910 | -0.2064326 | -0.3705440 | -0.1743270 | 0.3467216 | 0.4662719 | -0.0722737 | 0.0241195 | 0.1093305 |
mitch_report(res=mm2,outfile="multireactomestratified_all_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpDAn7eA/multireactomestratified_all_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/34
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## 21/34 [heatmap]## 22/34
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## 33/34 [session_info]
## 34/34## 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/RtmpDAn7eA/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/RtmpDAn7eA/rmarkdown-str383e39f542080.html##
## Output created: /tmp/RtmpDAn7eA/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,
"avb crplo t0"=avb_crplo_t0_adj, "avb crphi t0"=avb_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 | avb.crplo.t0 | avb.crphi.t0 | |
|---|---|---|---|---|
| Biosynthesis of Lipoxins (LX) | -0.3867545 | 0.4633187 | -0.8455452 | 0.3817386 |
| NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose | -0.6480768 | 0.3623051 | 0.2137571 | 0.7470112 |
| Formation of ATP by chemiosmotic coupling | -0.7990618 | 0.0543936 | -0.4210206 | 0.5772723 |
| Protein repair | -0.6253964 | -0.0012806 | -0.7807659 | 0.3025369 |
| Biosynthesis of E-series 18(S)-resolvins | -0.3304002 | 0.3824102 | -0.8379511 | 0.3230277 |
| Formation of annular gap junctions | -0.7470906 | 0.1117017 | -0.1898445 | 0.6685178 |
| Glycosphingolipid transport | -0.7715383 | 0.0083572 | -0.0215171 | 0.6716958 |
| Modulation by Mtb of host immune system | -0.8191726 | -0.0374605 | -0.4978862 | 0.2875243 |
| Peptide chain elongation | -0.8159484 | 0.1840574 | -0.3612197 | 0.3851253 |
| Classical antibody-mediated complement activation | -0.5800079 | 0.2416199 | -0.0504784 | 0.7615491 |
| Viral mRNA Translation | -0.8061665 | 0.1635394 | -0.3490062 | 0.3707051 |
| NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | -0.5768914 | 0.1882948 | 0.2346194 | 0.7150993 |
| Eukaryotic Translation Elongation | -0.7971197 | 0.1838313 | -0.3455162 | 0.3770319 |
| Scavenging of heme from plasma | -0.5409442 | 0.2791206 | -0.0912272 | 0.7387811 |
| Biosynthesis of EPA-derived SPMs | -0.1457952 | 0.3828973 | -0.8615075 | 0.1085346 |
| Creation of C4 and C2 activators | -0.5635405 | 0.2317873 | -0.0504570 | 0.7354446 |
| PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 | -0.6468699 | 0.3037932 | -0.2866139 | 0.5637487 |
| SARS-CoV-1 modulates host translation machinery | -0.7859480 | 0.1967726 | -0.3527271 | 0.3556863 |
| Phosphorylation of Emi1 | -0.3787200 | 0.1115837 | 0.3730638 | 0.7739054 |
| Formation of a pool of free 40S subunits | -0.7868557 | 0.1401860 | -0.3361004 | 0.3633714 |
| Fructose metabolism | -0.6674355 | 0.2927385 | -0.4698937 | 0.3434962 |
| Formyl peptide receptors bind formyl peptides and many other ligands | -0.6187035 | -0.2695029 | -0.5606798 | 0.3120406 |
| Eukaryotic Translation Termination | -0.7823269 | 0.1601891 | -0.3083629 | 0.3657818 |
| Diseases of Mismatch Repair (MMR) | 0.2591448 | -0.6835491 | 0.5531489 | -0.0673679 |
| Selenocysteine synthesis | -0.7670394 | 0.1543896 | -0.3062164 | 0.3647253 |
| Erythrocytes take up oxygen and release carbon dioxide | 0.4209134 | 0.5430898 | -0.4344391 | 0.4160650 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.7653626 | 0.1416099 | -0.2994770 | 0.3584066 |
| CD22 mediated BCR regulation | -0.5144714 | 0.3109448 | -0.0501061 | 0.6782824 |
| Prevention of phagosomal-lysosomal fusion | -0.6614875 | 0.1074415 | -0.2848553 | 0.5366076 |
| Initial triggering of complement | -0.5245789 | 0.2371696 | -0.0537770 | 0.6920181 |
| Nef Mediated CD4 Down-regulation | -0.6542193 | 0.1736781 | -0.0547754 | 0.5903512 |
| SRP-dependent cotranslational protein targeting to membrane | -0.7565149 | 0.0546858 | -0.3112007 | 0.3686715 |
| Glyoxylate metabolism and glycine degradation | -0.5337104 | 0.2109129 | -0.3005937 | 0.6203153 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.7511498 | 0.0906499 | -0.3321231 | 0.3407733 |
| VLDLR internalisation and degradation | -0.6602029 | 0.1635293 | -0.1365759 | 0.5604240 |
| FCGR activation | -0.5199340 | 0.2166411 | -0.0371101 | 0.6874476 |
| Cohesin Loading onto Chromatin | 0.1551784 | -0.6765142 | 0.5487008 | 0.0269991 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.7211841 | 0.1495516 | -0.3451626 | 0.3223475 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.7368549 | 0.0817513 | -0.3234099 | 0.3252264 |
| NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | -0.3966584 | 0.0672565 | 0.4351318 | 0.6384498 |
| Pentose phosphate pathway | -0.6339353 | -0.0635142 | -0.3574035 | 0.4668633 |
| SUMO is conjugated to E1 (UBA2:SAE1) | -0.6688223 | -0.4728013 | 0.0020032 | 0.2822685 |
| Cap-dependent Translation Initiation | -0.7219937 | 0.0843027 | -0.3263144 | 0.3316100 |
| Eukaryotic Translation Initiation | -0.7219937 | 0.0843027 | -0.3263144 | 0.3316100 |
| Synthesis of PIPs at the late endosome membrane | 0.3588079 | -0.6226643 | 0.3516629 | -0.3058985 |
| Synthesis of 5-eicosatetraenoic acids | -0.2730314 | 0.3411962 | -0.6909325 | 0.2535856 |
| Regulation of NFE2L2 gene expression | 0.0365360 | 0.4139260 | 0.4439210 | 0.5929352 |
| Retrograde neurotrophin signalling | -0.5940464 | 0.0922546 | -0.1446457 | 0.5821438 |
| Establishment of Sister Chromatid Cohesion | 0.1342114 | -0.6938394 | 0.4672051 | 0.0117821 |
| Role of LAT2/NTAL/LAB on calcium mobilization | -0.4987575 | 0.1888861 | -0.0659310 | 0.6455545 |
#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,
"avb crplo eos"=avb_crplo_eos_adj, "avb crphi eos"=avb_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 | avb.crplo.eos | avb.crphi.eos | |
|---|---|---|---|---|
| RUNX1 regulates transcription of genes involved in BCR signaling | 0.5562831 | 0.5473863 | -0.7500114 | -0.7757468 |
| Peptide chain elongation | -0.6817362 | -0.8467717 | 0.6603553 | 0.0087970 |
| Formation of xylulose-5-phosphate | -0.5771028 | -0.6573611 | 0.5938529 | 0.6981904 |
| Eukaryotic Translation Elongation | -0.6644667 | -0.8382738 | 0.6530513 | 0.0159410 |
| Formation of a pool of free 40S subunits | -0.6511485 | -0.8436330 | 0.6442221 | -0.0213781 |
| Viral mRNA Translation | -0.6690817 | -0.8311226 | 0.6409421 | -0.0086580 |
| SARS-CoV-1 modulates host translation machinery | -0.6478269 | -0.8201015 | 0.6416928 | -0.0368751 |
| Selenocysteine synthesis | -0.6490937 | -0.8080701 | 0.6339397 | 0.0075031 |
| Eukaryotic Translation Termination | -0.6569322 | -0.7940374 | 0.6410548 | -0.0067102 |
| Phenylalanine metabolism | -0.4335910 | -0.5975084 | 0.7369101 | 0.5580067 |
| L13a-mediated translational silencing of Ceruloplasmin expression | -0.6233642 | -0.8017651 | 0.5844671 | -0.0441766 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | -0.6201777 | -0.7993759 | 0.5856885 | -0.0503810 |
| Cap-dependent Translation Initiation | -0.6142199 | -0.8002121 | 0.5835718 | -0.0419248 |
| Eukaryotic Translation Initiation | -0.6142199 | -0.8002121 | 0.5835718 | -0.0419248 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | -0.6441316 | -0.7669802 | 0.5898119 | -0.0245771 |
| MET activates PI3K/AKT signaling | 0.7768482 | 0.3518596 | -0.5667546 | -0.5410203 |
| SRP-dependent cotranslational protein targeting to membrane | -0.6547592 | -0.7528227 | 0.5446763 | -0.0826633 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | -0.6197699 | -0.7547760 | 0.5730024 | -0.0136518 |
| Formation of ATP by chemiosmotic coupling | -0.8137176 | -0.7152782 | 0.2941717 | -0.1376996 |
| Formation of the ternary complex, and subsequently, the 43S complex | -0.5757066 | -0.7819498 | 0.5727102 | -0.0777560 |
| CD163 mediating an anti-inflammatory response | 0.0480724 | 0.2985498 | -0.7613764 | -0.7644889 |
| Mitochondrial translation initiation | -0.6774527 | -0.6965012 | 0.4756280 | -0.0641837 |
| Mitochondrial translation elongation | -0.6894478 | -0.6802714 | 0.4693414 | -0.0585665 |
| SARS-CoV-2 modulates host translation machinery | -0.5956580 | -0.6889368 | 0.5656083 | -0.0063335 |
| Mitochondrial translation termination | -0.6603892 | -0.6821002 | 0.4652994 | -0.0644525 |
| Ribosomal scanning and start codon recognition | -0.5604277 | -0.7322396 | 0.4966297 | -0.1035929 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | -0.5544103 | -0.7360382 | 0.4954529 | -0.0934320 |
| Translation initiation complex formation | -0.5512055 | -0.7315512 | 0.4970760 | -0.1005644 |
| Mitochondrial translation | -0.6409900 | -0.6716841 | 0.4665333 | -0.0619740 |
| APOBEC3G mediated resistance to HIV-1 infection | -0.4541966 | -0.5093935 | 0.7707920 | 0.1338001 |
| Selenoamino acid metabolism | -0.5591403 | -0.6956697 | 0.5292062 | -0.0234247 |
| Folding of actin by CCT/TriC | -0.5636182 | -0.5241985 | 0.5604439 | -0.3066169 |
| YAP1- and WWTR1 (TAZ)-stimulated gene expression | 0.2499870 | 0.6402718 | -0.5627891 | -0.4596477 |
| Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | -0.5284393 | -0.6620180 | 0.5283592 | -0.0414559 |
| Nonsense-Mediated Decay (NMD) | -0.5284393 | -0.6620180 | 0.5283592 | -0.0414559 |
| Regulation of expression of SLITs and ROBOs | -0.5355330 | -0.6597718 | 0.5009973 | -0.1047920 |
| Arachidonate production from DAG | -0.8172593 | -0.4496317 | -0.1967991 | 0.2641993 |
| Phosphate bond hydrolysis by NUDT proteins | -0.5383776 | -0.7731383 | 0.0518760 | -0.2936652 |
| Translation | -0.6010502 | -0.6188236 | 0.4698036 | -0.0595130 |
| LTC4-CYSLTR mediated IL4 production | 0.2796763 | -0.5653360 | 0.3885060 | 0.6466491 |
| Vpu mediated degradation of CD4 | -0.4668068 | -0.6472514 | 0.4827449 | -0.2853790 |
| RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) | 0.0382800 | 0.6761457 | -0.5626598 | -0.3959274 |
| Vif-mediated degradation of APOBEC3G | -0.5064480 | -0.6277394 | 0.4231337 | -0.3192836 |
| Complex III assembly | -0.6616111 | -0.6002240 | 0.3217027 | 0.0227125 |
| Classical antibody-mediated complement activation | -0.5762855 | 0.2384993 | -0.5379462 | 0.4698520 |
| Scavenging of heme from plasma | -0.5408181 | 0.2753379 | -0.5710090 | 0.4471092 |
| Regulation of activated PAK-2p34 by proteasome mediated degradation | -0.4718913 | -0.6080010 | 0.4272613 | -0.3357298 |
| Erythrocytes take up oxygen and release carbon dioxide | 0.3271060 | 0.5089513 | -0.3993270 | -0.6016863 |
| Cristae formation | -0.6654306 | -0.5625747 | 0.3298045 | -0.1158485 |
| Ubiquitin Mediated Degradation of Phosphorylated Cdc25A | -0.5150297 | -0.6187170 | 0.4134137 | -0.2480617 |
#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,
"avb crplo pod1"=avb_crplo_pod1_adj, "avb crphi pod1"=avb_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 | avb.crplo.pod1 | avb.crphi.pod1 | |
|---|---|---|---|---|
| MET activates PI3K/AKT signaling | 0.8254330 | -0.4128765 | 0.7083396 | -0.2995858 |
| Sulfide oxidation to sulfate | -0.6046310 | 0.2428840 | -0.7347703 | 0.5470256 |
| Establishment of Sister Chromatid Cohesion | 0.6802732 | -0.4141195 | 0.7730825 | 0.1289298 |
| CD163 mediating an anti-inflammatory response | 0.8177689 | 0.6035185 | -0.2169922 | -0.3801718 |
| Cohesin Loading onto Chromatin | 0.7608153 | -0.4192440 | 0.6718637 | -0.0912018 |
| Defects of platelet adhesion to exposed collagen | 0.0178692 | 0.6446714 | -0.7466152 | 0.4375833 |
| Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 0.7189564 | 0.5092484 | 0.4001506 | 0.4583863 |
| G2/M DNA replication checkpoint | 0.3610881 | 0.5359563 | 0.3615211 | 0.7507718 |
| Defective binding of VWF variant to GPIb:IX:V | 0.1990776 | 0.5923381 | -0.7481928 | 0.3913027 |
| Enhanced binding of GP1BA variant to VWF multimer:collagen | 0.1990776 | 0.5923381 | -0.7481928 | 0.3913027 |
| CD22 mediated BCR regulation | -0.3672206 | 0.5163059 | -0.1189545 | 0.8133555 |
| Erythrocytes take up oxygen and release carbon dioxide | 0.5902960 | 0.8004330 | 0.0711260 | 0.2812630 |
| Wax and plasmalogen biosynthesis | 0.5824736 | -0.6010919 | 0.5730422 | -0.1152485 |
| Phosphorylation of Emi1 | -0.1619366 | 0.6310224 | 0.0674448 | 0.7816476 |
| Scavenging of heme from plasma | -0.2942022 | 0.4724166 | -0.1092453 | 0.7784045 |
| NFE2L2 regulates pentose phosphate pathway genes | 0.7738644 | 0.4843493 | -0.2344199 | -0.1040127 |
| Activation of caspases through apoptosome-mediated cleavage | 0.3170644 | -0.5045104 | 0.6727067 | 0.2985676 |
| Classical antibody-mediated complement activation | -0.2987625 | 0.4468467 | -0.1224701 | 0.7541541 |
| Type I hemidesmosome assembly | 0.1201224 | 0.5509885 | -0.0846787 | 0.7228289 |
| ARMS-mediated activation | 0.5235406 | -0.3156838 | 0.6579439 | 0.1804176 |
| FCGR activation | -0.2545463 | 0.3941018 | -0.0164416 | 0.7723287 |
| Fructose metabolism | -0.4634688 | -0.3649494 | -0.6109789 | -0.2830516 |
| Creation of C4 and C2 activators | -0.2957188 | 0.4135281 | -0.1263310 | 0.7203392 |
| Biosynthesis of Lipoxins (LX) | 0.3713779 | 0.7323387 | -0.1977691 | 0.2655120 |
| Neurotransmitter clearance | 0.2082019 | 0.0614518 | -0.6183932 | -0.5650837 |
| Synthesis of PIPs at the late endosome membrane | 0.3813714 | -0.5026834 | 0.5608357 | -0.1882377 |
| Response to metal ions | 0.5293139 | 0.5816821 | 0.1614973 | 0.2812162 |
| Fructose catabolism | -0.4336032 | -0.2467244 | -0.6036521 | -0.3165286 |
| SMAC (DIABLO) binds to IAPs | 0.2033324 | -0.4876750 | 0.5428787 | 0.3550652 |
| SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes | 0.2033324 | -0.4876750 | 0.5428787 | 0.3550652 |
| SMAC, XIAP-regulated apoptotic response | 0.2033324 | -0.4876750 | 0.5428787 | 0.3550652 |
| SUMO is proteolytically processed | 0.1991967 | -0.5487990 | 0.5182222 | 0.2759605 |
| Scavenging by Class A Receptors | 0.6578167 | 0.1282681 | 0.2196206 | -0.4144047 |
| Initial triggering of complement | -0.2799182 | 0.3783384 | -0.1328510 | 0.6419002 |
| Common Pathway of Fibrin Clot Formation | 0.2776402 | 0.4569535 | -0.1834782 | 0.5754962 |
| Lysosphingolipid and LPA receptors | -0.4813277 | 0.3257954 | -0.3417757 | 0.4322397 |
| Unwinding of DNA | -0.3672928 | 0.2301995 | 0.0271331 | 0.6684870 |
| Mitotic Telophase/Cytokinesis | 0.5578661 | -0.1762784 | 0.5238809 | 0.1139577 |
| Regulation of IFNG signaling | 0.5575592 | -0.0247187 | 0.5526222 | -0.0013251 |
| Role of LAT2/NTAL/LAB on calcium mobilization | -0.2033667 | 0.3194894 | -0.0095182 | 0.6860033 |
| STAT5 activation downstream of FLT3 ITD mutants | 0.5944999 | 0.4826252 | 0.0123015 | -0.1456307 |
| MET activates RAP1 and RAC1 | 0.6576378 | -0.1930142 | 0.3386527 | -0.1340959 |
| Maturation of protein 3a_9683673 | 0.1829222 | 0.3807820 | 0.2558003 | 0.5932969 |
| Maturation of protein 3a_9694719 | 0.1829222 | 0.3807820 | 0.2558003 | 0.5932969 |
| Maturation of hRSV A proteins | 0.5255686 | -0.3835289 | 0.3964436 | -0.1108648 |
| OAS antiviral response | -0.1582490 | -0.3463050 | 0.5183573 | 0.4216875 |
| Protein repair | 0.4695722 | 0.1666118 | -0.0330243 | 0.5620244 |
| Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane | 0.2936538 | 0.5563768 | -0.2654458 | 0.3115986 |
| Transport of connexons to the plasma membrane | 0.2936538 | 0.5563768 | -0.2654458 | 0.3115986 |
| Butyrophilin (BTN) family interactions | -0.4953255 | -0.2848091 | -0.4092831 | -0.2621852 |
#mitch_report(res=mm2,outfile="multireactomestratified_pod1_mitchreport.html",overwrite=TRUE)Session information
For reproducibility
sessionInfo()## R version 4.4.1 (2024-06-14)
## 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
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## 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] pkgload_1.4.0 GGally_2.2.1
## [3] beeswarm_0.4.0 gtools_3.9.5
## [5] tibble_3.2.1 echarts4r_0.4.5
## [7] xlsx_0.6.5 DT_0.33
## [9] eulerr_7.0.2 ggplot2_3.5.1
## [11] kableExtra_1.4.0 MASS_7.3-61
## [13] mitch_1.17.4 DESeq2_1.44.0
## [15] SummarizedExperiment_1.34.0 Biobase_2.64.0
## [17] MatrixGenerics_1.16.0 matrixStats_1.4.1
## [19] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
## [21] IRanges_2.38.1 S4Vectors_0.42.1
## [23] BiocGenerics_0.50.0 dplyr_1.1.4
## [25] WGCNA_1.73 fastcluster_1.2.6
## [27] dynamicTreeCut_1.63-1 reshape2_1.4.4
## [29] gplots_3.2.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.8.9
## [4] magrittr_2.0.3 farver_2.1.2 rmarkdown_2.28
## [7] zlibbioc_1.50.0 vctrs_0.6.5 memoise_2.0.1.9000
## [10] base64enc_0.1-3 progress_1.2.3 htmltools_0.5.8.1
## [13] S4Arrays_1.4.1 SparseArray_1.4.8 Formula_1.2-5
## [16] sass_0.4.9 KernSmooth_2.23-24 bslib_0.8.0
## [19] htmlwidgets_1.6.4 plyr_1.8.9 impute_1.78.0
## [22] cachem_1.1.0 mime_0.12 lifecycle_1.0.4
## [25] iterators_1.0.14 pkgconfig_2.0.3 Matrix_1.7-0
## [28] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.12
## [31] shiny_1.9.1 digest_0.6.37 colorspace_2.1-1
## [34] AnnotationDbi_1.66.0 Hmisc_5.1-3 RSQLite_2.3.7
## [37] labeling_0.4.3 fansi_1.0.6 httr_1.4.7
## [40] abind_1.4-8 compiler_4.4.1 bit64_4.5.2
## [43] withr_3.0.1 doParallel_1.0.17 htmlTable_2.4.3
## [46] backports_1.5.0 BiocParallel_1.38.0 DBI_1.2.3
## [49] ggstats_0.7.0 highr_0.11 DelayedArray_0.30.1
## [52] caTools_1.18.3 tools_4.4.1 foreign_0.8-87
## [55] httpuv_1.6.15 nnet_7.3-19 glue_1.8.0
## [58] promises_1.3.0 grid_4.4.1 checkmate_2.3.2
## [61] cluster_2.1.6 generics_0.1.3 gtable_0.3.5
## [64] preprocessCore_1.66.0 tidyr_1.3.1 hms_1.1.3
## [67] data.table_1.16.0 xml2_1.3.6 utf8_1.2.4
## [70] XVector_0.44.0 foreach_1.5.2 pillar_1.9.0
## [73] stringr_1.5.1 later_1.3.2 rJava_1.0-11
## [76] splines_4.4.1 lattice_0.22-6 survival_3.7-0
## [79] bit_4.5.0 tidyselect_1.2.1 GO.db_3.19.1
## [82] locfit_1.5-9.10 Biostrings_2.72.1 knitr_1.48
## [85] gridExtra_2.3 svglite_2.1.3 xfun_0.48
## [88] stringi_1.8.4 UCSC.utils_1.0.0 yaml_2.3.10
## [91] xlsxjars_0.6.1 evaluate_1.0.1 codetools_0.2-20
## [94] cli_3.6.3 rpart_4.1.23 xtable_1.8-4
## [97] systemfonts_1.1.0 munsell_0.5.1 jquerylib_0.1.4
## [100] Rcpp_1.0.13 png_0.1-8 parallel_4.4.1
## [103] blob_1.2.4 prettyunits_1.2.0 bitops_1.0-9
## [106] viridisLite_0.4.2 scales_1.3.0 purrr_1.0.2
## [109] crayon_1.5.3 rlang_1.1.4 KEGGREST_1.44.1