date generated: 2020-07-11

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 -7.3024303

Here are some metrics about the input data profile:

Profile metrics
Profile metrics
num_genesets 6
num_genes_in_profile 16428
duplicated_genes_present 0
num_profile_genes_in_sets 426
num_profile_genes_not_in_sets 16002

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: atac.gmt

Gene sets metrics
Gene sets metrics
num_genesets 6
num_genesets_excluded 0
num_genesets_included 6

Differential pathway expression


Interactive enrichment scatterplot

Significance is calculated by -log10(p-value). All points shown are FDR<0.05.

Significance is calculated by -log10(p-value). Top N sets shown irrespective of FDR.

Results table

Top N= 6 gene sets

set setSize pANOVA s.dist p.adjustANOVA
ATAC enhancer down 141 4.10e-10 -0.305 2.46e-09
ATAC tss up 94 2.33e-09 0.357 7.00e-09
ATAC enhancer up 88 7.36e-08 0.332 1.47e-07
ATAC tss down 112 9.71e-07 -0.268 1.46e-06
ATAC enhancer down with TEAD motif 28 4.84e-02 -0.216 5.81e-02
ATAC enhancer up with TEAD motif 14 9.55e-02 0.257 9.55e-02


Results (complete table)


Click HERE to show results for all gene sets

Complete results
set setSize pANOVA s.dist p.adjustANOVA
ATAC enhancer down 141 4.10e-10 -0.305 2.46e-09
ATAC tss up 94 2.33e-09 0.357 7.00e-09
ATAC enhancer up 88 7.36e-08 0.332 1.47e-07
ATAC tss down 112 9.71e-07 -0.268 1.46e-06
ATAC enhancer down with TEAD motif 28 4.84e-02 -0.216 5.81e-02
ATAC enhancer up with TEAD motif 14 9.55e-02 0.257 9.55e-02



Detailed Gene set reports



ATAC enhancer down

ATAC enhancer down
2
set ATAC enhancer down
setSize 141
pANOVA 4.1e-10
s.dist -0.305
p.adjustANOVA 2.46e-09



Top enriched genes

Top 20 genes
GeneID Gene Rank
Prima1 -7903
Dkk3 -7902
Fgf1 -7869
Nr3c1 -7849
Sgk1 -7848
Slc2a3 -7813
Fam160b1 -7799
Mdga1 -7754
Adrb2 -7747
Crim1 -7734
Dhrs3 -7704
Pdlim5 -7702
Gpt2 -7636
Siah1a -7569
Setbp1 -7532
Adamts2 -7507
Sorbs3 -7495
Fkbp5 -7491
Nphp4 -7480
Idh2 -7440

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
Prima1 -7903
Dkk3 -7902
Fgf1 -7869
Nr3c1 -7849
Sgk1 -7848
Slc2a3 -7813
Fam160b1 -7799
Mdga1 -7754
Adrb2 -7747
Crim1 -7734
Dhrs3 -7704
Pdlim5 -7702
Gpt2 -7636
Siah1a -7569
Setbp1 -7532
Adamts2 -7507
Sorbs3 -7495
Fkbp5 -7491
Nphp4 -7480
Idh2 -7440
Cachd1 -7386
Man2a1 -7350
Ankrd9 -7320
Rbm20 -7300
Sema7a -7248
Arrdc2 -7211
Glul -7169
Mpped2 -7076
Prkce -6989
Fam78b -6987
Mtus1 -6945
Enho -6847
Klf13 -6817
0610038B21Rik -6787
Ndufa6 -6776
Ankrd26 -6689
Creg1 -6687
Zfp385b -6646
Snta1 -6630
Rhobtb1 -6431
Nt5dc1 -6388
Rgma -6383
Max -6319
Gbe1 -6277
Trdn -6270
Fzd7 -6260
Ppp1r12b -6258
Tbc1d1 -6252
Zbtb16 -6213
Sorl1 -6136
Pgm2 -6115
Cdc14a -5998
Ptprm -5918
Fam13c -5865
Kremen1 -5811
Ehd3 -5785
Igsf3 -5713
Plekha7 -5624
Shroom3 -5611
Gm826 -5552
Pln -5379
Dapk2 -5257
1700123O20Rik -4963
Fbxo3 -4848
Klhl25 -4749
Rpia -4633
Synpo2 -4532
Plbd2 -4438
Cltc -4154
2310015A10Rik -4000
Farp2 -3880
Eef2k -3817
Afg3l2 -3703
Ddx20 -3608
Napb -3432
Fyco1 -3285
Itsn2 -3149
Ticam1 -2999
Ebf3 -2965
Tpst2 -2934
Trim32 -2887
Prkca -2874
Cish -2749
Stard8 -2260
Dnaic2 -2249
Ccdc158 -2161
Arid5b -1908
Ggcx -1713
Ankrd46 -1617
Cd79b -1475
Pde4dip -1019
Rpl29 -985
Msi2 -953
Hopx -769
Brpf3 -749
Rell1 -316
Lpin1 5
Aff1 390
Fntb 520
Pmp22 718
Larp1 1117
Tmem229b 1195
Eepd1 1250
Bicd2 1358
Npc1 1744
Atp13a1 2360
Fcer1g 2509
Rcc2 2741
Agt 2763
Slc36a1 2799
Slc41a3 2834
Tns1 2906
Srpk1 3349
Dnajc17 3724
Grin2b 3847
Tmem123 4507
Abtb1 4925
Ap1s1 4989
Bcl6 5510
Bmp7 5560
Heg1 6182
Timp3 6221
Impa2 6238
Crip1 6522
Fbn1 6586
Fnbp1 6614
Rps6ka4 6720
Flnb 6745
Ckap4 6772
Acvrl1 6799
Phf1 7069
Rab31 7168
Chaf1b 7216
Cdc7 7456
Gnb4 7484
Thbs1 7600
Trerf1 8015
Ptprj 8187
Litaf 8272
Usp18 8324
Lair1 8499



ATAC tss up

ATAC tss up
3
set ATAC tss up
setSize 94
pANOVA 2.33e-09
s.dist 0.357
p.adjustANOVA 7e-09



Top enriched genes

Top 20 genes
GeneID Gene Rank
Irf1 8514
Mx2 8430
Psmb9 8393
Pik3r5 8375
Irgm1 8366
B2m 8156
Knstrn 8131
Bid 8078
Scamp5 8052
Rgs14 7955
Zc3hav1 7853
Icosl 7652
Rps6ka1 7619
Chaf1a 7602
Arap1 7584
Orai2 7577
Lasp1 7556
Map3k8 7555
Prex1 7451
Cdc6 7295

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
Irf1 8514
Mx2 8430
Psmb9 8393
Pik3r5 8375
Irgm1 8366
B2m 8156
Knstrn 8131
Bid 8078
Scamp5 8052
Rgs14 7955
Zc3hav1 7853
Icosl 7652
Rps6ka1 7619
Chaf1a 7602
Arap1 7584
Orai2 7577
Lasp1 7556
Map3k8 7555
Prex1 7451
Cdc6 7295
Phldb1 7206
Zdhhc18 7072
Gramd2 7014
Tbx1 6981
Serpinb9 6970
Nxpe3 6939
Car9 6886
Src 6850
Utrn 6753
Cks2 6608
Rab3d 6433
Capg 6403
Arhgap23 6384
Id3 6370
Gstt2 6093
Nfix 6087
Gps2 6040
Gm30771 6022
Wsb2 6010
Arhgef40 5910
Hmgb3 5700
Prtg 5559
Rnpep 5432
Herc3 5072
Lin9 4979
Vps9d1 4958
Myo15b 4792
Frmd8 4678
Oscp1 4673
Ccdc69 4633
Aprt 4394
Psd3 4332
Pus1 4295
Noc4l 4199
Cd248 3716
Anp32a 3140
Dus2 2884
Slc36a1 2799
Ramp1 2777
Fbxw4 2776
Sf3a3 2673
Gm24753 2285
Gls 2152
Itga2b 1988
Dpf1 1844
Esr1 1658
Cpeb1 855
Mrpl20 552
Calu 176
Mtch1 82
Gars -90
Msto1 -349
Bckdk -402
Neb -595
Plgrkt -669
Ppil2 -792
Zfp384 -1088
Erlin1 -1255
Arl10 -1636
Timm17a -3226
Tmem70 -3647
Ift81 -3755
Sspn -4441
Caml -4538
Zfp286 -4976
Matr3 -5145
Ttc28 -5150
Thnsl2 -5228
Bcdin3d -5872
Gm49258 -6163
Ly6g6e -6355
Zfp346 -6856
Dmxl1 -7114
9130230L23Rik -7330



ATAC enhancer up

ATAC enhancer up
1
set ATAC enhancer up
setSize 88
pANOVA 7.36e-08
s.dist 0.332
p.adjustANOVA 1.47e-07



Top enriched genes

Top 20 genes
GeneID Gene Rank
Card14 8425
Gsdmd 8394
Prkch 8376
Dhx58 8276
Batf 8126
Cd83 7804
Olfm1 7779
Runx1 7737
Csrp1 7723
Arap1 7584
Rfc5 7452
Prex1 7451
Als2cl 7333
Dusp5 7274
9130019P16Rik 6947
Farp1 6710
Dusp10 6708
Arl5c 6704
Capn1 6699
Srcin1 6652

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
Card14 8425
Gsdmd 8394
Prkch 8376
Dhx58 8276
Batf 8126
Cd83 7804
Olfm1 7779
Runx1 7737
Csrp1 7723
Arap1 7584
Rfc5 7452
Prex1 7451
Als2cl 7333
Dusp5 7274
9130019P16Rik 6947
Farp1 6710
Dusp10 6708
Arl5c 6704
Capn1 6699
Srcin1 6652
Cbx2 6495
Anxa4 6456
Begain 6445
Spsb1 6437
Itga11 6423
Capg 6403
Tmbim6 6245
Tpm2 6217
Ppp1r14c 5985
Uchl1 5739
Lrrc49 5479
Fbln2 5257
Klf16 5231
Eif4g3 4884
Entpd7 4705
Ccdc69 4633
Dgkd 4548
Gtf3c6 4515
Tmem123 4507
Rnf114 4088
Dffa 4001
Bmf 3930
Wnt9a 3798
Ppargc1b 3670
Sim2 3565
Sh2d4a 3424
Ncoa3 3400
Cspg4 3313
Myh10 3309
Anp32a 3140
Sfxn2 2994
Bhlhe41 2842
Ramp1 2777
Agt 2763
Trim47 2761
Recql5 2605
Raph1 2570
Col4a2 2506
Apbb2 2486
Sufu 2239
Ncor2 2179
Gls 2152
Dnajb12 2121
Afap1l1 2017
Dpf1 1844
Xylt1 1510
Manbal 517
Rnf103 373
Calu 176
Svil 139
Mtch1 82
Zfp36l1 -450
Camk2a -473
Zeb2 -592
Ky -1240
Pigv -1484
Cables2 -1879
Cstad -2620
Tst -2968
Trap1 -4501
Jak1 -5538
Col20a1 -6149
I830077J02Rik -6660
Gpc1 -6707
Dnajb1 -6836
Lpp -7207
Slc30a2 -7276
D430041D05Rik -7701



ATAC tss down

ATAC tss down
4
set ATAC tss down
setSize 112
pANOVA 9.71e-07
s.dist -0.268
p.adjustANOVA 1.46e-06



Top enriched genes

Top 20 genes
GeneID Gene Rank
Htra1 -7906
Gm15337 -7904
Cryab -7892
8430426J06Rik -7886
Gm48630 -7879
Ell2 -7839
Cntfr -7833
Odf3l2 -7821
Gm29323 -7805
Eci2 -7772
Tmem52 -7766
Lrif1 -7711
Cobll1 -7700
Hsph1 -7695
Napa -7692
Slc35f5 -7642
D830013O20Rik -7610
9530020I12Rik -7608
Gm11827 -7575
Gm43672 -7551

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
Htra1 -7906
Gm15337 -7904
Cryab -7892
8430426J06Rik -7886
Gm48630 -7879
Ell2 -7839
Cntfr -7833
Odf3l2 -7821
Gm29323 -7805
Eci2 -7772
Tmem52 -7766
Lrif1 -7711
Cobll1 -7700
Hsph1 -7695
Napa -7692
Slc35f5 -7642
D830013O20Rik -7610
9530020I12Rik -7608
Gm11827 -7575
Gm43672 -7551
Setbp1 -7532
Tsc22d3 -7527
Sorbs3 -7495
6430571L13Rik -7478
Sec14l1 -7417
Chac1 -7415
Jrkl -7339
Ankrd9 -7320
Glb1l2 -7307
Gm15169 -7267
Arrdc2 -7211
Musk -7173
Hspa8 -7147
Klf13 -6817
Stab2 -6788
Zrsr1 -6642
Pde4d -6546
Rhobtb1 -6431
Max -6319
Tet1 -6217
Bhlhe40 -6098
Ndufs2 -6017
Gm826 -5552
Pde4a -5350
Impact -5346
Fbxo9 -4954
Morf4l2 -4803
Senp7 -4782
Gm38074 -4240
Shld1 -4178
Pcdh9 -3947
Clcn1 -3501
Hdac9 -3239
5430425K12Rik -3103
Polr3b -2896
Tkt -2560
Ubr3 -2393
Abt1 -2342
2310001H17Rik -2265
Nt5dc3 -2100
Mir155hg -2015
Bbs2 -1983
Mpp7 -1859
Gm37257 -1815
Larp4b -1434
Sephs1 -1420
Pde4dip -1019
Rab10os -954
Pex7 -693
Phc1 -429
Tyw1 -175
2410080I02Rik 51
Hoxa10 345
Fam207a 352
Gm32569 364
Xkr6 511
Haus7 730
Dnal1 758
Myom3 2218
Crebzf 2745
Tns1 2906
Trrap 3146
Rps23 3262
Slc24a3 3595
Car5b 3645
Unkl 3999
Gm10800 4026
Fxn 4151
4930505A04Rik 4170
Tacc2 4600
Pakap 4639
Cux2 4650
Ctnna2 4719
Gm10801 4774
Awat2 4955
Mta1 5050
Epha3 5079
Gm5444 5296
Eda2r 5650
Gm21738 5707
Kcnip1 5753
Exo5 6109
Gm11872 6174
Gabre 6468
Mt2 6626
Ppp2r3d 6833
Plekhg1 6996
Grip2 7263
Fam189a1 7465
Frmd4b 7570
Tns3 7876
Litaf 8272



ATAC enhancer down with TEAD motif

ATAC enhancer down with TEAD motif
5
set ATAC enhancer down with TEAD motif
setSize 28
pANOVA 0.0484
s.dist -0.216
p.adjustANOVA 0.0581



Top enriched genes

Top 20 genes
GeneID Gene Rank
Dkk3 -7902
Gm973 -7858
Mdga1 -7754
Adrb2 -7747
Idh2 -7440
Cachd1 -7386
Ghr -7193
Klf13 -6817
Fzd7 -6260
AW549877 -6216
Igsf3 -5713
Zfyve19 -4484
Napb -3432
Tpst2 -2934
Hopx -769
Rell1 -316
Lpin1 5
Itgb5 374
Vps18 778
Ilf3 2169

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
Dkk3 -7902
Gm973 -7858
Mdga1 -7754
Adrb2 -7747
Idh2 -7440
Cachd1 -7386
Ghr -7193
Klf13 -6817
Fzd7 -6260
AW549877 -6216
Igsf3 -5713
Zfyve19 -4484
Napb -3432
Tpst2 -2934
Hopx -769
Rell1 -316
Lpin1 5
Itgb5 374
Vps18 778
Ilf3 2169
Tns1 2906
Dnajc17 3724
Slc44a2 4542
Trim41 5975
Heg1 6182
Rps6ka4 6720
Thbs1 7600
Irgm1 8366



ATAC enhancer up with TEAD motif

ATAC enhancer up with TEAD motif
6
set ATAC enhancer up with TEAD motif
setSize 14
pANOVA 0.0955
s.dist 0.257
p.adjustANOVA 0.0955



Top enriched genes

Top 20 genes
GeneID Gene Rank
Batf 8126
Ablim3 6919
Kcnq2 5946
Itgb4 5941
Eef1a2 5696
Bmf 3930
Wnt9a 3798
Galk1 3692
Raph1 2570
Ncor2 2179
Afap1l1 2017
Trap1 -4501
Col20a1 -6149
Chrna4 -6294

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
Batf 8126
Ablim3 6919
Kcnq2 5946
Itgb4 5941
Eef1a2 5696
Bmf 3930
Wnt9a 3798
Galk1 3692
Raph1 2570
Ncor2 2179
Afap1l1 2017
Trap1 -4501
Col20a1 -6149
Chrna4 -6294



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_0.5.0

END of report