Mitch Report
Antony Kaspi & Mark Ziemann
date generated: 2020-08-06
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.
## x
## 0610005C13Rik 0.5455811
## 0610009B22Rik -0.2758387
## 0610009E02Rik -0.1942335
## 0610009L18Rik 0.6285430
## 0610010F05Rik -1.9585193
## 0610012D04Rik -7.3024303Here are some metrics about the input data profile:
| Profile metrics | |
|---|---|
| num_genesets | 26 |
| num_genes_in_profile | 16428 |
| duplicated_genes_present | 0 |
| num_profile_genes_in_sets | 67 |
| num_profile_genes_not_in_sets | 16361 |
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: promoter_motifs.gmt
| Gene sets metrics | |
|---|---|
| num_genesets | 26 |
| num_genesets_excluded | 23 |
| num_genesets_included | 3 |
Differential pathway expression
Interactive enrichment scatterplot
Significance is calculated by -log10(p-value). All points shown are FDR<0.05.
Results table
Top N= 3 gene sets
| set | setSize | pANOVA | s.dist | p.adjustANOVA |
|---|---|---|---|---|
| motif12.motif.bed TEAD2(TEA) | 12 | 0.01830 | -0.393 | 0.0275 |
| motif7.motif.bed NF1-halfsite(CTF) | 24 | 0.00888 | -0.309 | 0.0266 |
| motif2.motif.bed PGR(NR) | 15 | 0.65300 | -0.067 | 0.6530 |
Results (complete table)
Click HERE to show results for all gene sets
| set | setSize | pANOVA | s.dist | p.adjustANOVA |
|---|---|---|---|---|
| motif12.motif.bed TEAD2(TEA) | 12 | 0.01830 | -0.393 | 0.0275 |
| motif7.motif.bed NF1-halfsite(CTF) | 24 | 0.00888 | -0.309 | 0.0266 |
| motif2.motif.bed PGR(NR) | 15 | 0.65300 | -0.067 | 0.6530 |
Detailed Gene set reports
motif12.motif.bed_TEAD2(TEA)
| 1 | |
|---|---|
| set | motif12.motif.bed_TEAD2(TEA) |
| setSize | 12 |
| pANOVA | 0.0183 |
| s.dist | -0.393 |
| p.adjustANOVA | 0.0275 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| 8430426J06Rik | -7886 |
| Napa | -7692 |
| Gm15169 | -7267 |
| Arrdc2 | -7211 |
| Gm826 | -5552 |
| Impact | -5346 |
| Fbxo9 | -4954 |
| Ick | -4328 |
| Pcdh9 | -3947 |
| Gm10800 | 4026 |
| Ppp2r3d | 6833 |
| Litaf | 8272 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| 8430426J06Rik | -7886 |
| Napa | -7692 |
| Gm15169 | -7267 |
| Arrdc2 | -7211 |
| Gm826 | -5552 |
| Impact | -5346 |
| Fbxo9 | -4954 |
| Ick | -4328 |
| Pcdh9 | -3947 |
| Gm10800 | 4026 |
| Ppp2r3d | 6833 |
| Litaf | 8272 |
motif7.motif.bed_NF1-halfsite(CTF)
| 3 | |
|---|---|
| set | motif7.motif.bed_NF1-halfsite(CTF) |
| setSize | 24 |
| pANOVA | 0.00888 |
| s.dist | -0.309 |
| p.adjustANOVA | 0.0266 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Odf3l2 | -7821 |
| Gm29323 | -7805 |
| Tmem52 | -7766 |
| D830013O20Rik | -7610 |
| Apoo | -7420 |
| Glb1l2 | -7307 |
| Gm15169 | -7267 |
| Rhobtb1 | -6431 |
| Max | -6319 |
| Gm826 | -5552 |
| Impact | -5346 |
| Gm38074 | -4240 |
| Pcdh9 | -3947 |
| Abt1 | -2342 |
| Nt5dc3 | -2100 |
| Larp4b | -1434 |
| Pex7 | -693 |
| Gm32569 | 364 |
| Gm26836 | 5243 |
| Gm5444 | 5296 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Odf3l2 | -7821 |
| Gm29323 | -7805 |
| Tmem52 | -7766 |
| D830013O20Rik | -7610 |
| Apoo | -7420 |
| Glb1l2 | -7307 |
| Gm15169 | -7267 |
| Rhobtb1 | -6431 |
| Max | -6319 |
| Gm826 | -5552 |
| Impact | -5346 |
| Gm38074 | -4240 |
| Pcdh9 | -3947 |
| Abt1 | -2342 |
| Nt5dc3 | -2100 |
| Larp4b | -1434 |
| Pex7 | -693 |
| Gm32569 | 364 |
| Gm26836 | 5243 |
| Gm5444 | 5296 |
| Kcnip1 | 5753 |
| Exo5 | 6109 |
| Plekhg1 | 6996 |
| Litaf | 8272 |
motif2.motif.bed_PGR(NR)
| 2 | |
|---|---|
| set | motif2.motif.bed_PGR(NR) |
| setSize | 15 |
| pANOVA | 0.653 |
| s.dist | -0.067 |
| p.adjustANOVA | 0.653 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Napa | -7692 |
| Tet1 | -6217 |
| Bhlhe40 | -6098 |
| Mettl5 | -4756 |
| Clcn1 | -3501 |
| Bbs2 | -1983 |
| Gm37257 | -1815 |
| Pex7 | -693 |
| Tyw1 | -175 |
| Dnal1 | 758 |
| Crebzf | 2745 |
| Awat2 | 4955 |
| Exo5 | 6109 |
| Grip2 | 7263 |
| Fam189a1 | 7465 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Napa | -7692 |
| Tet1 | -6217 |
| Bhlhe40 | -6098 |
| Mettl5 | -4756 |
| Clcn1 | -3501 |
| Bbs2 | -1983 |
| Gm37257 | -1815 |
| Pex7 | -693 |
| Tyw1 | -175 |
| Dnal1 | 758 |
| Crebzf | 2745 |
| Awat2 | 4955 |
| Exo5 | 6109 |
| Grip2 | 7263 |
| Fam189a1 | 7465 |
Here is the session info with all the versions of packages used.
sessionInfo()## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
##
## 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
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] pkgload_1.1.0 GGally_2.0.0
## [3] beeswarm_0.2.3 gtools_3.8.2
## [5] echarts4r_0.3.2 mitch_1.0.6
## [7] MASS_7.3-51.6 fgsea_1.14.0
## [9] gplots_3.0.3 DESeq2_1.28.1
## [11] SummarizedExperiment_1.18.1 DelayedArray_0.14.0
## [13] matrixStats_0.56.0 Biobase_2.48.0
## [15] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
## [17] IRanges_2.22.2 S4Vectors_0.26.1
## [19] BiocGenerics_0.34.0 reshape2_1.4.4
## [21] forcats_0.5.0 stringr_1.4.0
## [23] dplyr_1.0.0 purrr_0.3.4
## [25] readr_1.3.1 tidyr_1.1.0
## [27] tibble_3.0.1 ggplot2_3.3.2
## [29] tidyverse_1.3.0
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.4-1 ellipsis_0.3.1 rprojroot_1.3-2
## [4] XVector_0.28.0 fs_1.4.2 rstudioapi_0.11
## [7] bit64_0.9-7 AnnotationDbi_1.50.1 fansi_0.4.1
## [10] lubridate_1.7.9 xml2_1.3.2 splines_4.0.2
## [13] geneplotter_1.66.0 knitr_1.29 jsonlite_1.7.0
## [16] broom_0.5.6 annotate_1.66.0 dbplyr_1.4.4
## [19] shiny_1.5.0 compiler_4.0.2 httr_1.4.1
## [22] backports_1.1.8 assertthat_0.2.1 Matrix_1.2-18
## [25] fastmap_1.0.1 cli_2.0.2 later_1.1.0.1
## [28] htmltools_0.5.0 tools_4.0.2 gtable_0.3.0
## [31] glue_1.4.1 GenomeInfoDbData_1.2.3 fastmatch_1.1-0
## [34] Rcpp_1.0.4.6 cellranger_1.1.0 vctrs_0.3.1
## [37] gdata_2.18.0 nlme_3.1-148 xfun_0.15
## [40] testthat_2.3.2 rvest_0.3.5 mime_0.9
## [43] lifecycle_0.2.0 XML_3.99-0.3 zlibbioc_1.34.0
## [46] scales_1.1.1 hms_0.5.3 promises_1.1.1
## [49] RColorBrewer_1.1-2 yaml_2.2.1 memoise_1.1.0
## [52] gridExtra_2.3 reshape_0.8.8 stringi_1.4.6
## [55] RSQLite_2.2.0 highr_0.8 genefilter_1.70.0
## [58] desc_1.2.0 caTools_1.18.0 BiocParallel_1.22.0
## [61] rlang_0.4.6 pkgconfig_2.0.3 bitops_1.0-6
## [64] evaluate_0.14 lattice_0.20-41 htmlwidgets_1.5.1
## [67] bit_1.1-15.2 tidyselect_1.1.0 plyr_1.8.6
## [70] magrittr_1.5 R6_2.4.1 generics_0.0.2
## [73] DBI_1.1.0 pillar_1.4.4 haven_2.3.1
## [76] withr_2.2.0 survival_3.2-3 RCurl_1.98-1.2
## [79] modelr_0.1.8 crayon_1.3.4 KernSmooth_2.23-17
## [82] rmarkdown_2.3 locfit_1.5-9.4 grid_4.0.2
## [85] readxl_1.3.1 data.table_1.12.8 blob_1.2.1
## [88] reprex_0.3.0 digest_0.6.25 pbmcapply_1.5.0
## [91] xtable_1.8-4 httpuv_1.5.4 munsell_0.5.0END of report