Mitch Report
Antony Kaspi & Mark Ziemann
date generated: 2024-11-26
Background
Mitch performs unidimensional and multidimensional gene set enrichment analysis. The concept behind this dates to work by Cox and Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). This implementation is suited to R based workflows of multi-omics datasets. This software was developed by Antony Kaspi and Mark Ziemann. Learn more about Mitch at the website: https://github.com/markziemann/Mitch
Input profiles
Here is the first few lines of the input profile.
| rna2 | k9a2 | |
|---|---|---|
| A2M | 3.415090 | 2.7880123 |
| AAAS | -2.962096 | 3.4898251 |
| ABRA | 10.673777 | 13.3060357 |
| AC004453.8 | -2.076975 | 0.8679133 |
| AC006480.1 | -2.155952 | 1.8189543 |
| AC013437.7 | -3.810378 | -0.0657374 |
Here are some metrics about the input data profile:
| Profile metrics | |
|---|---|
| num_genes_in_profile | 1000 |
| duplicated_genes_present | 0 |
| num_profile_genes_in_sets | 192 |
| num_profile_genes_not_in_sets | 808 |
| profile_pearson_correl | 0.23499 |
| profile_spearman_correl | 0.22935 |
Here is a plot of the input profiles. Note the dynamic ranges.
Here is the contour plot of the profile including all detected genes.
Input genesets
Here are some metrics about the gene sets used:
GMT file of genesets:| Gene sets metrics | |
|---|---|
| num_genesets | 200 |
| num_genesets_excluded | 195 |
| num_genesets_included | 5 |
Gene sets by quadrant
Number of significant gene sets (FDR<0.05)= 1
Interactive enrichment scatterplot
All sets with FDR<0.05. Try hovering over the points.
Top N sets irrespective of FDR. Try hovering over the points.
A heatmap of S values for top results
A plot of effect size versus significance
Significance is the -log2(p.adjustMANOVA) and effect size is the
s.dist which is the hypotenuse of the s scores.
Results table
Top N= 3 gene sets| set | setSize | pMANOVA | p.adjustMANOVA | s.dist | s.rna2 | s.k9a2 | p.rna2 | p.k9a2 |
|---|---|---|---|---|---|---|---|---|
| Biological oxidations | 10 | 0.0090 | 0.045 | 0.5570 | -0.5560 | -0.0414 | 0.00243 | 0.8220 |
| Antigen processing: Ubiquitination & Proteasome degradation | 20 | 0.0597 | 0.149 | 0.2890 | -0.0555 | 0.2840 | 0.67100 | 0.0296 |
| Adaptive Immune System | 44 | 0.5300 | 0.672 | 0.0978 | 0.0000 | 0.0978 | 1.00000 | 0.2730 |
Results (complete table)
Click HERE to show results for all gene sets
| set | setSize | pMANOVA | p.adjustMANOVA | s.dist | s.rna2 | s.k9a2 | p.rna2 | p.k9a2 |
|---|---|---|---|---|---|---|---|---|
| Biological oxidations | 10 | 0.0090 | 0.045 | 0.5570 | -0.55600 | -0.0414 | 0.00243 | 0.8220 |
| Antigen processing: Ubiquitination & Proteasome degradation | 20 | 0.0597 | 0.149 | 0.2890 | -0.05550 | 0.2840 | 0.67100 | 0.0296 |
| Adaptive Immune System | 44 | 0.5300 | 0.672 | 0.0978 | 0.00000 | 0.0978 | 1.00000 | 0.2730 |
| Asparagine N-linked glycosylation | 17 | 0.5380 | 0.672 | 0.1440 | -0.13600 | 0.0459 | 0.33600 | 0.7450 |
| Axon guidance | 48 | 0.9450 | 0.945 | 0.0264 | 0.00696 | -0.0255 | 0.93500 | 0.7650 |
Detailed Gene set reports
Biological oxidations
| metric | value |
|---|---|
| setSize | 10 |
| pMANOVA | 0.009 |
| p.adjustMANOVA | 0.045 |
| s.dist | 0.557 |
| s.rna2 | -0.556 |
| s.k9a2 | -0.0414 |
| p.rna2 | 0.00243 |
| p.k9a2 | 0.822 |
| Gene | rna2 | k9a2 |
|---|---|---|
| GGT5 | -188 | -74 |
Click HERE to show all gene set members
| rna2 | k9a2 | |
|---|---|---|
| BPHL | -12 | 386 |
| CES3 | -293 | 87 |
| CYP2J2 | -218 | 480 |
| GGT5 | -188 | -74 |
| GSS | -203 | 726 |
| GSTM2 | -295 | 361 |
| GSTP1 | -131 | 276 |
| HSP90AB1 | 327 | 851 |
| MTR | 219 | 526 |
| SULT1A1 | -152 | 11 |
Antigen processing: Ubiquitination & Proteasome degradation
| metric | value |
|---|---|
| setSize | 20 |
| pMANOVA | 0.0597 |
| p.adjustMANOVA | 0.149 |
| s.dist | 0.289 |
| s.rna2 | -0.0555 |
| s.k9a2 | 0.284 |
| p.rna2 | 0.671 |
| p.k9a2 | 0.0296 |
| Gene | rna2 | k9a2 |
|---|---|---|
| PSMB7 | -268 | 620 |
| UBE2E3 | -125 | 557 |
| WSB1 | -137 | 508 |
| ANAPC7 | -206 | 326 |
| PSMA4 | -99 | 610 |
| PSMB5 | -209 | 97 |
Click HERE to show all gene set members
| rna2 | k9a2 | |
|---|---|---|
| ANAPC7 | -206 | 326 |
| ASB7 | 130 | 262 |
| FBXL14 | 286 | 579 |
| HECTD1 | 196 | 771 |
| HERC1 | 382 | 769 |
| HERC2 | 318 | 3 |
| HUWE1 | 221 | 525 |
| ITCH | 263 | 452 |
| LTN1 | 24 | 671 |
| NEDD4 | 185 | 869 |
| PJA2 | 297 | 764 |
| PSMA4 | -99 | 610 |
| PSMB5 | -209 | 97 |
| PSMB7 | -268 | 620 |
| RNF19A | 161 | 677 |
| TRIP12 | 343 | 407 |
| UBE2C | 647 | 127 |
| UBE2E3 | -125 | 557 |
| WSB1 | -137 | 508 |
| ZBTB16 | 657 | 857 |
Adaptive Immune System
| metric | value |
|---|---|
| setSize | 44 |
| pMANOVA | 0.53 |
| p.adjustMANOVA | 0.672 |
| s.dist | 0.0978 |
| s.rna2 | 0 |
| s.k9a2 | 0.0978 |
| p.rna2 | 1 |
| p.k9a2 | 0.273 |
| Gene | rna2 | k9a2 |
|---|---|---|
| PSMB7 | -268 | 620 |
| UBE2E3 | -125 | 557 |
| WSB1 | -137 | 508 |
| ANAPC7 | -206 | 326 |
| BTN3A1 | -155 | 403 |
| PSMA4 | -99 | 610 |
| PSMB5 | -209 | 97 |
Click HERE to show all gene set members
| rna2 | k9a2 | |
|---|---|---|
| ANAPC7 | -206 | 326 |
| ASB7 | 130 | 262 |
| BTN3A1 | -155 | 403 |
| BTN3A2 | -109 | -8 |
| CHUK | 178 | 397 |
| DYNC1H1 | 266 | 273 |
| ENAH | 366 | 811 |
| ERAP1 | 175 | 241 |
| FBXL14 | 286 | 579 |
| HECTD1 | 196 | 771 |
| HERC1 | 382 | 769 |
| HERC2 | 318 | 3 |
| HUWE1 | 221 | 525 |
| ICAM1 | 557 | 30 |
| ITCH | 263 | 452 |
| KRAS | 362 | 472 |
| LTN1 | 24 | 671 |
| MRC1 | 14 | 76 |
| NEDD4 | 185 | 869 |
| NFATC3 | 155 | 491 |
| NFKBIA | 177 | 712 |
| PAK2 | 93 | 563 |
| PIK3CA | 235 | 388 |
| PIK3CB | 399 | 494 |
| PIK3R3 | 637 | 444 |
| PJA2 | 297 | 764 |
| PPP2R1B | 10 | 773 |
| PSMA4 | -99 | 610 |
| PSMB5 | -209 | 97 |
| PSMB7 | -268 | 620 |
| PTPN11 | 89 | 182 |
| RICTOR | 192 | 753 |
| RIPK2 | 308 | -21 |
| RNF19A | 161 | 677 |
| SEC24A | 72 | 96 |
| TAP1 | 158 | 261 |
| TNFRSF14 | -290 | -92 |
| TRIP12 | 343 | 407 |
| UBE2C | 647 | 127 |
| UBE2E3 | -125 | 557 |
| VASP | 490 | 445 |
| WSB1 | -137 | 508 |
| YES1 | 497 | 295 |
| ZBTB16 | 657 | 857 |
Here is the session info with all the versions of packages used.
sessionInfo()## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## 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=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] kableExtra_1.4.0 pkgload_1.4.0 GGally_2.2.1 ggplot2_3.5.1
## [5] reshape2_1.4.4 beeswarm_0.4.0 gplots_3.2.0 gtools_3.9.5
## [9] tibble_3.2.1 dplyr_1.1.4 echarts4r_0.4.5 stringi_1.8.4
## [13] mitch_1.19.2
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.9 utf8_1.2.4 generics_0.1.3 tidyr_1.3.1
## [5] bitops_1.0-9 xml2_1.3.6 KernSmooth_2.23-24 caTools_1.18.3
## [9] digest_0.6.37 magrittr_2.0.3 evaluate_1.0.1 grid_4.4.2
## [13] RColorBrewer_1.1-3 fastmap_1.2.0 plyr_1.8.9 jsonlite_1.8.9
## [17] gridExtra_2.3 promises_1.3.1 purrr_1.0.2 fansi_1.0.6
## [21] viridisLite_0.4.2 scales_1.3.0 jquerylib_0.1.4 cli_3.6.3
## [25] shiny_1.9.1 rlang_1.1.4 munsell_0.5.1 withr_3.0.2
## [29] cachem_1.1.0 yaml_2.3.10 parallel_4.4.2 tools_4.4.2
## [33] colorspace_2.1-1 httpuv_1.6.15 ggstats_0.7.0 vctrs_0.6.5
## [37] R6_2.5.1 mime_0.12 lifecycle_1.0.4 stringr_1.5.1
## [41] htmlwidgets_1.6.4 MASS_7.3-61 pkgconfig_2.0.3 pillar_1.9.0
## [45] bslib_0.8.0 later_1.4.0 gtable_0.3.6 glue_1.8.0
## [49] Rcpp_1.0.13-1 systemfonts_1.1.0 xfun_0.49 tidyselect_1.2.1
## [53] rstudioapi_0.17.1 knitr_1.49 farver_2.1.2 xtable_1.8-4
## [57] htmltools_0.5.8.1 labeling_0.4.3 rmarkdown_2.29 svglite_2.1.3
## [61] compiler_4.4.2END of report