## Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
## 'DelayedArray::makeNindexFromArrayViewport' when loading 'SummarizedExperiment'
## create a temporary directory for the GSEA database files
temp_dir <- tempdir()
#temp_dir <- "/Users/hungm/Documents/development/deseq2pip/inst/extdata/"
Create gene set collections for run_gsea()
# create gene set collections for human and mouse
collection_name <- c("HALLMARK", "GOBP", "KEGG", "REACTOME", "BIOCARTA", "TFT")
for(i in c("hs_gs", "mm_gs")){
if(i == "hs_gs"){
org = "Homo sapiens"}
else if(i == "mm_gs"){
org = "Mus musculus"}
gs <- list()
# c1 gene set
HM<-msigdbr(species = org, category ="H")
gs[[1]] <- HM %>% dplyr::select(., gs_name, gene_symbol) %>% mutate(collection = collection_name[1])
# c5 gene set
GO<-msigdbr(species = org, category ="C5")
gs[[2]] <-GO %>% dplyr::select(., gs_name, gene_symbol) %>% filter(stringr::str_detect(gs_name, 'GOBP')) %>% mutate(collection = collection_name[2])
# c2 gene set
C2<-msigdbr(species = org, category ="C2")
gs[[3]] <-C2 %>% dplyr::select(., gs_name, gene_symbol) %>% filter(stringr::str_detect(gs_name, 'KEGG')) %>% mutate(collection = collection_name[3])
gs[[4]] <-C2 %>% dplyr::select(., gs_name, gene_symbol) %>% filter(stringr::str_detect(gs_name, 'REACTOME')) %>% mutate(collection = collection_name[4])
gs[[5]] <-C2 %>% dplyr::select(., gs_name, gene_symbol) %>% filter(stringr::str_detect(gs_name, 'BIOCARTA')) %>% mutate(collection = collection_name[5])
# c3 gene set
TFT <-msigdbr(species = org, category ="C3")
gs[[6]] <-TFT %>% dplyr::select(., gs_name, gene_symbol) %>% mutate(collection = collection_name[6])
gs <- bind_rows(gs)
assign(i, gs)}
## Warning: The `category` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
## ℹ Please use the `collection` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# Save TSV files to temporary directory
write.table(mm_gs, file.path(temp_dir, "20250319_mouse_msigdbr.tsv"), sep = "\t", quote = F, row.names = F)
write.table(hs_gs, file.path(temp_dir, "20250319_human_msigdbr.tsv"), sep = "\t", quote = F, row.names = F)
# show the first few rows of the human and mouse gene set collections
head(hs_gs)
## # A tibble: 6 × 3
## gs_name gene_symbol collection
## <chr> <chr> <chr>
## 1 HALLMARK_ADIPOGENESIS ABCA1 HALLMARK
## 2 HALLMARK_ADIPOGENESIS ABCB8 HALLMARK
## 3 HALLMARK_ADIPOGENESIS ACAA2 HALLMARK
## 4 HALLMARK_ADIPOGENESIS ACADL HALLMARK
## 5 HALLMARK_ADIPOGENESIS ACADM HALLMARK
## 6 HALLMARK_ADIPOGENESIS ACADS HALLMARK
## # A tibble: 6 × 3
## gs_name gene_symbol collection
## <chr> <chr> <chr>
## 1 HALLMARK_ADIPOGENESIS Abca1 HALLMARK
## 2 HALLMARK_ADIPOGENESIS Abcb8 HALLMARK
## 3 HALLMARK_ADIPOGENESIS Acaa2 HALLMARK
## 4 HALLMARK_ADIPOGENESIS Acadl HALLMARK
## 5 HALLMARK_ADIPOGENESIS Acadm HALLMARK
## 6 HALLMARK_ADIPOGENESIS Acads HALLMARK
Create GMT files for EnrichmentMap
# convert mouse gene set collection to a list of gene symbols
gs_name <- mm_gs$gs_name
mm_gs_list <- mm_gs %>%
select(-c(collection, gs_name)) %>%
.$gene_symbol %>%
split(., gs_name)
mm_gs_list %>% head(.)
## $AAACCAC_MIR140
## [1] "Abcc4" "Abraxas2" "Actn4" "Acvr1"
## [5] "Adam9" "Adamts5" "Amer2" "Ank2"
## [9] "Api5" "Atosa" "Bach1" "Baz2b"
## [13] "Bcl11a" "Bcl2l2" "Bcl9" "Bmt2"
## [17] "1700025G04Rik" "Cacna1c" "Cebpa" "Chd4"
## [21] "Cit" "Col23a1" "Csk" "Csnk1g3"
## [25] "Ctcf" "Cul3" "Dazl" "Dbndd2"
## [29] "Dcun1d4" "Ddx3x" "Ddx3y" "Dhx57"
## [33] "Dipk2a" "Dpp4" "Dscam" "Dtna"
## [37] "E2f3" "Ehd1" "Ephb1" "Erc2"
## [41] "Etv3" "Eya2" "Gabarap" "Galnt16"
## [45] "Gdf6" "Git1" "Gys1" "Hdac4"
## [49] "Hnrnph3" "Hspa13" "Igfbp5" "Katnbl1"
## [53] "Kcnd2" "Loxl3" "Lrrc4" "Lrrc8e"
## [57] "Map3k8" "Mdga2" "Mex3c" "Mgat1"
## [61] "Mmd" "Mok" "Nav3" "Nkiras2"
## [65] "Nr3c1" "Nsd3" "Nutf2" "Ogt"
## [69] "Ostm1" "Pdgfra" "Pfn1" "Phf20l1"
## [73] "Phyhip" "Pitx2" "Ppp1cc" "Prima1"
## [77] "R3hdm1" "Reep1" "Rnf19a" "Rtkn2"
## [81] "Senp1" "Siah1a" "Slc25a13" "Slc38a2"
## [85] "Slc41a2" "Slf2" "Slmap" "Snx2"
## [89] "Sox4" "Srr" "Stag1" "Stradb"
## [93] "Syt6" "Taf9b" "Tbx3" "Trp53inp2"
## [97] "Tshz1" "Tspan2" "Tssk2" "Ttyh2"
## [101] "Ubash3b" "Usp32" "Vegfa" "Wnt1"
## [105] "Yes1" "Zbed4" "Zbtb10" "Zfp182"
## [109] "Zfp608" "Zfp654"
##
## $AAAGACA_MIR511
## [1] "Abcg8" "Ace" "Adamtsl3" "Adgrf5"
## [5] "Adss" "Agbl3" "Ago1" "Ago2"
## [9] "Ago4" "Alcam" "Anapc15" "Ankrd40cl"
## [13] "Ankzf1" "Aqp6" "Arhgef17" "Atl2"
## [17] "Atp2b2" "Atrx" "Bcl11a" "Btg1"
## [21] "Bub3" "C1ql2" "1700025G04Rik" "Calm1"
## [25] "Camk2n1" "Camta1" "Caprin1" "Ccdc178"
## [29] "Ccnd1" "Ccnt2" "Cdh2" "Cdk14"
## [33] "Cdk19" "Celf1" "Celf6" "Cep350"
## [37] "Cfap298" "Clk2" "Cltc" "Cnot4"
## [41] "Corin" "Crebrf" "Crem" "Crim1"
## [45] "Dctn4" "Ddx3x" "Ddx3y" "Dedd"
## [49] "Dnajb12" "Dnajc13" "Dsc1" "Dusp6"
## [53] "Dyrk1b" "E2f3" "Edem3" "Efr3a"
## [57] "Elavl3" "Emilin2" "Eml4" "Enpp1"
## [61] "Enpp4" "Epha4" "Esrrg" "Eya1"
## [65] "Eya4" "Fam117a" "Fgf13" "Fip1l1"
## [69] "Fmr1" "Fn1" "Fndc1" "Fndc5"
## [73] "Foxk2" "Foxn3" "Gad2" "Gemin2"
## [77] "Gfap" "Gja1" "Glra2" "Has2"
## [81] "Hcn4" "Hlf" "Hltf" "Hoxa13"
## [85] "Igf2bp1" "Igf2bp3" "Ilrun" "Kcne1"
## [89] "Kcnma1" "Khdrbs2" "Klf9" "Klhl18"
## [93] "Klhl24" "Lats1" "Lmcd1" "Lpp"
## [97] "Lrch4" "Luc7l3" "Map3k2" "Map4k4"
## [101] "Mapk1ip1l" "Mbd2" "Mbd6" "Mdga2"
## [105] "Metap2" "Mib1" "Mink1" "Mrpl21"
## [109] "Mstn" "Mtap" "Mycbp" "Myo19"
## [113] "Naa50" "Nacc1" "Neurod6" "Nhlh2"
## [117] "Nlk" "Nr4a2" "Nrxn3" "Ntrk2"
## [121] "Nxph1" "Onecut2" "Pax8" "Pcare"
## [125] "Pcdh10" "Pcdh17" "Peli1" "Phaf1"
## [129] "Phlpp1" "Pik3r3" "Pmepa1" "Pogk"
## [133] "Pou4f2" "Ppargc1a" "Prelp" "Prpf4b"
## [137] "Psma1" "Psmd10" "Zadh2" "Qki"
## [141] "Rab22a" "Rab2a" "Rbm15b" "Rbm26"
## [145] "Reck" "Rev3l" "Rgl1" "Rhoj"
## [149] "Rhot1" "Rnf19a" "Robo2" "Rps6kb1"
## [153] "Rps6kl1" "Satb2" "Scn4b" "Selenop"
## [157] "Sema3f" "Sema6d" "Sinhcaf" "Slc22a17"
## [161] "Slc25a26" "Slc6a6" "Slitrk1" "Smarce1"
## [165] "Socs2" "Sorcs3" "Sost" "Sox12"
## [169] "Sptbn4" "Sptlc2" "Srgap3" "Ss18"
## [173] "St18" "Syt11" "Taf5" "T"
## [177] "Thoc5" "Tial1" "Tmem196" "Tmem243"
## [181] "Tmem248" "Tnrc6a" "Tnrc6b" "Tob1"
## [185] "Trappc3" "Trappc8" "Trim2" "Trim24"
## [189] "Tspoap1" "Txnl1" "Ube2h" "Vangl2"
## [193] "Vav3" "Virma" "Vkorc1l1" "Vmp1"
## [197] "Wnt16" "Ythdf2" "Yy1" "Zcchc24"
## [201] "Zdhhc21" "Zfp319" "Zfp654" "Zfp706"
##
## $AAAGGAT_MIR501
## [1] "Acaca" "Acadsb" "Adcyap1" "Adipor2"
## [5] "Als2" "Alx1" "Ammecr1" "Apold1"
## [9] "Atp6v1h" "Bcl6" "Bclaf1" "C030006K11Rik"
## [13] "Cachd1" "Camta1" "Cblif" "Cd164"
## [17] "Cdk2ap1" "Celf2" "Celsr2" "Chodl"
## [21] "Clk1" "Clk2" "Ctdsp1" "Ctdspl2"
## [25] "Cul1" "Cux2" "Dcx" "Dnajb12"
## [29] "Elavl4" "Errfi1" "Grb10" "H2ax"
## [33] "Has2" "Hes5" "Hoxb8" "Jade3"
## [37] "Jun" "Kcnd2" "Kcnrg" "Kif1c"
## [41] "Kif2a" "Klhl14" "Krr1" "Larp1"
## [45] "Leprotl1" "Lpgat1" "Lpin1" "Lrrc1"
## [49] "Map2k1" "Map3k8" "Mcu" "Mef2c"
## [53] "Myb" "Mycl" "Mylk" "Nexmif"
## [57] "Nfasc" "Nfil3" "Nfix" "Npr3"
## [61] "Nr2f2" "Nr4a3" "Pcdh19" "Pdk1"
## [65] "Phc1" "Phf6" "Pik3ap1" "Pitx2"
## [69] "Plp1" "Plxnb1" "Pnn" "Ppp1cb"
## [73] "Ppp2r5e" "Ppp4r3a" "Ppp6r3" "Prkce"
## [77] "Pura" "Qki" "Rab22a" "Rabgef1"
## [81] "Rasl10b" "Rcn1" "Rdx" "Ret"
## [85] "Rgl1" "Rnf11" "Robo2" "Rpgrip1l"
## [89] "Rsbn1" "Satb2" "Scn3a" "Senp3"
## [93] "Sephs1" "Sgpp1" "Slc25a3" "Slc35b3"
## [97] "Slitrk5" "Smc1a" "Snap29" "Sox11"
## [101] "Sox4" "Spopl" "Srr" "Srsf2"
## [105] "Sync" "Synj1" "Syt7" "Taf5l"
## [109] "Tapt1" "Tnni2" "Togaram1" "Tomm70a"
## [113] "Trim39" "Tsc22d3" "Ubap1" "Ube2q1"
## [117] "Ube4b" "Usp12" "Vdac2" "Wdfy3"
## [121] "Wipf2" "Zbtb18" "Zc3h7a" "Zic4"
## [125] "Zmym5"
##
## $AAAGGGA_MIR204_MIR211
## [1] "Abraxas2" "Adamts9" "Adcy6" "Adprm"
## [5] "Ago4" "Akap1" "Alpl" "Angpt1"
## [9] "Ankrd13a" "Anxa11" "Ap1s1" "Ap1s3"
## [13] "Ap2a2" "Ap3m1" "Aph1a" "Arap2"
## [17] "Arcn1" "Arglu1" "Arhgap29" "Arl8b"
## [21] "Atf2" "Atp2b1" "Aup1" "Baz2a"
## [25] "Bcl11b" "Bcl2" "Bcl9" "Bcl9l"
## [29] "Brd4" "Brpf3" "Caprin1" "Ccdc120"
## [33] "Ccnt2" "Ccpg1" "Cdc25b" "Cdc42"
## [37] "Cdh2" "Celsr3" "Chd5" "Chn2"
## [41] "Chp1" "Clip1" "Coro1c" "Cox5a"
## [45] "Cpd" "Cpne8" "Creb5" "Crkl"
## [49] "Ctdnep1" "Dag1" "Dcaf5" "Dcun1d3"
## [53] "Dennd5a" "Dhh" "Dlg5" "Dmtf1"
## [57] "Dnajc13" "Dnm2" "Dtx1" "Dvl3"
## [61] "Dyrk1a" "Edem1" "Eef1e1" "Efnb3"
## [65] "Elavl3" "Elf2" "Ell2" "Elmod3"
## [69] "Elovl6" "Epha7" "Ephb6" "Esr1"
## [73] "Esrrg" "Eva1c" "Ezr" "Fam117b"
## [77] "Fam120c" "Farp1" "Fbn2" "Fbxw7"
## [81] "Fhip1b" "Fjx1" "Fnip1" "Fras1"
## [85] "Frem1" "Fry" "Gabrb3" "Gapvd1"
## [89] "Gga2" "Glis3" "Gpm6a" "Grm1"
## [93] "1810013L24Rik" "Hic2" "Hmga2" "Hook3"
## [97] "Hoxc8" "Hs2st1" "Igf2r" "Ing4"
## [101] "Itpr1" "Jph3" "Kcna3" "Kctd1"
## [105] "Kdm2a" "Khdrbs1" "Khdrbs3" "Kitl"
## [109] "Klf12" "Klhl13" "Kmt2a" "Kmt5a"
## [113] "Lats1" "Lpar1" "Lrrc8d" "Mall"
## [117] "Maml3" "Map1lc3b" "Map3k3" "Mbnl1"
## [121] "Med13l" "Metap1" "Mllt3" "Mmgt1"
## [125] "Mon2" "Mrpl35" "Mrpl52" "Myo10"
## [129] "Naa15" "Nbea" "Ncoa7" "Neurog1"
## [133] "Nova1" "Nptx1" "Nr3c1" "Nr4a2"
## [137] "Nrbf2" "Ntrk2" "P4hb" "Fam122b"
## [141] "Pcdh9" "Phf13" "Pid1" "Plag1"
## [145] "Pou3f2" "Ppargc1a" "Ppp3r1" "Prdm2"
## [149] "Prpf38b" "Prrx1" "Rab10" "Rab14"
## [153] "Rab1a" "Rap2c" "Rbsn" "Reep1"
## [157] "Rere" "Rhobtb3" "Rhot1" "Rictor"
## [161] "Rps6ka3" "Rps6ka5" "Rps6kc1" "Rspo3"
## [165] "Rtkn2" "Runx2" "Satb2" "Scrt2"
## [169] "Sec24d" "Sec61a2" "Serinc3" "Sf3b1"
## [173] "Sgcz" "Sgip1" "Shc1" "Sin3a"
## [177] "Sirt1" "Slc17a7" "Slc22a2" "Slc37a3"
## [181] "Slitrk4" "Sltm" "Smoc1" "Socs6"
## [185] "Sox11" "Sox4" "Spop" "Spred1"
## [189] "Spryd7" "Ssrp1" "St7" "Stxbp5"
## [193] "Sumo2" "Sumo2" "Szrd1" "Taf5"
## [197] "Tcf12" "Tcf7l1" "Tgfbr2" "Tmem30a"
## [201] "Tmod3" "Tnrc6b" "Trp53inp1" "Triap1"
## [205] "Trip12" "Trpc5" "Ttyh1" "Ube2r2"
## [209] "Uhrf2" "Usp32" "Wee1" "Wnt4"
## [213] "Wsb1" "Xrn1" "Ythdf3" "Ywhag"
## [217] "Zcchc14" "Zcchc24" "Zdhhc17" "Zfc3h1"
## [221] "Zfp91" "Zfp282" "Zfp335" "Zfp423"
##
## $AAANWWTGC_UNKNOWN
## [1] "Actb" "Adhfe1" "Aff4" "Ank2" "Ank3" "App"
## [7] "Aspa" "Atoh7" "Atp1b1" "Atp2b4" "Atxn7l1" "Bcl11a"
## [13] "Bcl6" "Bnc2" "AI593442" "Cacna1d" "Cacng3" "Calm1"
## [19] "Cd14" "Cdc42ep3" "Cdc42ep5" "Cdh13" "Cdk2ap1" "Cept1"
## [25] "Chd2" "Cited2" "Cnmd" "Cntfr" "Dab1" "Dcaf11"
## [31] "Dchs2" "Ddit3" "Dis3l" "Dlg2" "Dlgap4" "Dmd"
## [37] "Dnajb5" "Dpysl5" "Drd3" "Dscam" "Dsel" "Dstn"
## [43] "Dtx3l" "Dusp1" "Dync1i2" "Ebf1" "Efna5" "Egflam"
## [49] "Eif4ebp2" "Elavl4" "Elf4" "Epha7" "Ephb2" "Esr1"
## [55] "Fam78a" "Fbxw7" "Fgf7" "Fgfr2" "Fn1" "Foxn3"
## [61] "Foxp1" "Foxp2" "Fthl17a" "Fzd7" "Ganab" "Gata3"
## [67] "Glra2" "Gpc3" "Gpc6" "Gpr21" "Gprin3" "Grhl3"
## [73] "Grin2b" "Gtf2e2" "Hepacam" "Hhex" "Hoxa2" "Hoxa3"
## [79] "Hoxb2" "Hoxb6" "Hoxc4" "Igf2bp1" "Inhba" "Itm2c"
## [85] "Jade2" "Kank1" "Kcnj13" "Klf12" "Klf14" "Krtap8-1"
## [91] "Leap2" "Lipg" "Lox" "Loxl4" "Lrrc3b" "Lrrn1"
## [97] "Lsamp" "Luc7l3" "Maml3" "Man2a2" "Map3k4" "Mapk3"
## [103] "Mbnl1" "Mef2c" "Meis1" "Mgll" "Mid1" "Mllt6"
## [109] "Mmp3" "Mpzl3" "Mrap" "Mrpl24" "Mrps18b" "Mycl"
## [115] "Myh2" "Mylk" "Ncbp3" "Nek6" "Neurog1" "Nfe2l2"
## [121] "Nnat" "Nr2f2" "Nras" "Ntn1" "Ntrk3" "Olfm1"
## [127] "Olig2" "Omg" "Otx2" "Parp9" "Patz1" "Pax1"
## [133] "Pax6" "Pcsk1" "Pctp" "Pdgfrb" "Phox2b" "Phtf1"
## [139] "Pik3r3" "Pou2f1" "Pou4f1" "Ppargc1a" "Ppfia2" "Ppp1r10"
## [145] "Ppp2r2a" "Ppp3cc" "Prdm16" "Prima1" "Prpf4b" "Rab10"
## [151] "Rbmx" "Rora" "Rrs1" "Rspo2" "S100pbp" "Sall3"
## [157] "Samd12" "Satb2" "Sema6c" "Sesn2" "Sfrp2" "Sgcd"
## [163] "Shc3" "Six5" "Skil" "Skp2" "Slmap" "Sncaip"
## [169] "Snx25" "Sort1" "Sox13" "Sox4" "Sox5" "Spag9"
## [175] "Sparcl1" "Ssbp3" "Steap2" "Tbc1d8b" "Tfap4" "Tfdp2"
## [181] "Tgif1" "Thap12" "Thbs2" "Tle4" "Tlk1" "Tlx3"
## [187] "Tram1" "Trpm3" "Spacdr" "Zfpm1" "Zhx3" "Zfp462"
## [193] "Zfp827" "Zw10"
##
## $AAAYRNCTG_UNKNOWN
## [1] "Abt1" "Acvr1" "Adam12" "Add3" "Adgrb3" "Aggf1"
## [7] "Ankrd12" "Ankrd28" "Ap4s1" "Apbb2" "Apobr" "Aqp2"
## [13] "Arhgap44" "Arid1a" "Arid4a" "Arpc2" "Arsg" "Arx"
## [19] "Asb4" "Asph" "Atoh8" "Atp1a2" "Atpif1" "Atp5l"
## [25] "Axdnd1" "B4galt6" "Bambi" "Bcl2l1" "Bcl9" "Bmpr1b"
## [31] "Bmx" "Brsk2" "Btbd3" "Bub3" "Car3" "Cacna2d3"
## [37] "Cacnb2" "Capn1" "Capza1" "Casq2" "Cbx2" "Ccdc174"
## [43] "Ccnj" "Ccny" "Cdc23" "Cdh2" "Cer1" "Cfap161"
## [49] "Chrm1" "Cited2" "Cldn5" "Cltc" "Cltrn" "Cmklr1"
## [55] "Cntln" "Cntn1" "Coch" "Col12a1" "Col1a2" "Col4a5"
## [61] "Col4a6" "Colec10" "Crat" "Crh" "Crkl" "Crygd"
## [67] "Crygs" "Csnk1a1" "Csrnp3" "Cstf3" "Cybrd1" "Cyria"
## [73] "Daam1" "Dbndd2" "Dcakd" "Ddah2" "Ddx4" "Def6"
## [79] "Dennd4a" "Dgkb" "Dhh" "Dhrs4" "Dhrs4" "Dido1"
## [85] "Dmd" "Dmrt1" "Dnaja2" "Dnajb4" "Dscaml1" "Dusp4"
## [91] "Dync1i1" "Dyrk1a" "Eda" "Efna1" "Egflam" "Eif5"
## [97] "Emx2" "Epc1" "Epha7" "Erbb4" "Erg28" "Errfi1"
## [103] "Esrp2" "Esrrb" "Esrrg" "Eya1" "Fam216b" "Fam83f"
## [109] "Fcer1a" "Fgd4" "Fgf10" "Fgf12" "Fgfr1" "Fgfr1op2"
## [115] "Fiz1" "Fkrp" "Fmnl3" "Fndc9" "Foxa1" "Foxg1"
## [121] "Foxo4" "Foxp2" "Fsip2" "Fst" "Gabra3" "Gdnf"
## [127] "Gfi1" "Ggnbp2" "Gjb4" "Gldn" "Gnaq" "Gpr85"
## [133] "Gprc5d" "Grin2b" "Gse1" "H3f3a" "Hdac8" "Hesx1"
## [139] "Hexim2" "Hgf" "Hic2" "Hid1" "Hip1r" "Hoxa10"
## [145] "Hoxa5" "Hoxb8" "Hpse2" "Hsd3b7" "Icam4" "Id1"
## [151] "Igf1" "Il1rapl1" "Inhbc" "Ip6k2" "Itga10" "Itga8"
## [157] "Jade2" "Jph1" "Jpt1" "Kank2" "Kcnip2" "Kcnk5"
## [163] "Kcnn3" "Kitl" "Klf5" "Klhdc10" "Klhl20" "Klhl3"
## [169] "Kmt2a" "Lars2" "Leng9" "Lhfp" "Lhx9" "Lix1"
## [175] "Lmo7" "Lrp5" "Lrrc4" "Lrrn4cl" "Ltbp1" "Maml1"
## [181] "Manf" "Map2" "Map3k5" "Map6" "Meis1" "Mgat1"
## [187] "Mgat4a" "Mid1" "Moap1" "Mpped2" "Mrpl13" "Mta2"
## [193] "Mtbp" "Mtrfr" "Myf6" "Myh1" "Myh10" "Myo18a"
## [199] "Naglu" "Napb" "Nav2" "Nav3" "Ncdn" "Ndnf"
## [205] "Ndst4" "Ndufs4" "Nek1" "Nek2" "Nfatc4" "Nfyb"
## [211] "Nmi" "Nmt1" "Nr2f1" "Nrg1" "Ntrk2" "Nup54"
## [217] "Nxph4" "Oma1" "Omg" "Or2l13" "Otx2" "Pacrg"
## [223] "Pals2" "Pcdh17" "Pcdh18" "Pcf11" "Pcyt1b" "Pdgfb"
## [229] "Pdgfra" "Pdlim2" "Pds5b" "Pdzrn4" "Pfn2" "Phc2"
## [235] "Phex" "Phf1" "Phf6" "Phox2b" "Plagl2" "Plec"
## [241] "Plekhm1" "Plp2" "Plpp3" "Pmch" "Podxl2" "Pofut1"
## [247] "Pou2af1" "Pou4f1" "Ppp1r9b" "Ppp2r3a" "Ppp2r5e" "Ppp3ca"
## [253] "Prelp" "Prkcg" "Prkcq" "Prkn" "Prok2" "Ptchd4"
## [259] "Zadh2" "Pth1r" "Ptpa" "Pxn" "R3hdm1" "Rab30"
## [265] "Rab5b" "Rab5c" "Rapgef4" "Rbms3" "Rgs17" "Rnf146"
## [271] "Robo4" "Ror1" "Rplp0" "Rtn1" "S1pr2" "Scn3b"
## [277] "Scn5a" "Scn8a" "Scoc" "Sdcbp" "Sema6d" "Septin7"
## [283] "Sesn3" "Sgcd" "Sh2d6" "Shc3" "Shcbp1l" "Sipa1"
## [289] "Sirpa" "Slc26a6" "Slc4a1" "Slc6a1" "Smarca2" "Snx9"
## [295] "Sorbs2" "Sox12" "Sox21" "Sox30" "Sox5" "Spindoc"
## [301] "Spock2" "Sptlc2" "Srgap2" "Srsf2" "Ssbp2" "St7l"
## [307] "Stac3" "Stag1" "Stag2" "Stc2" "Strn3" "Strn4"
## [313] "Tas1r2" "Tef" "Tent4b" "Tfap4" "Tfdp2" "Tm2d3"
## [319] "Tmem182" "Tmem69" "Tmsb4x" "Tnfaip8" "Tns1" "Tnxb"
## [325] "Trp53inp2" "Trdn" "Treml1" "Trim28" "Trim68" "Trim8"
## [331] "Triml1" "Trps1" "Tsc22d3" "Tspan7" "Tssk3" "Ttc17"
## [337] "Tusc2" "Ube2w" "Ubxn10" "Usp1" "Vdr" "Vip"
## [343] "Vkorc1l1" "Vwa5a" "Wbp1" "Wnt2b" "Wt1" "Xrcc1"
## [349] "Zbtb11" "Zbtb18" "Zfp91" "Zfpm2" "Zic1" "Zic4"
## [355] "Zmat3" "Zfp296" "Zfp503" "Zfp521" "Zfp524" "Zfp654"
## [361] "Zfp687" "Zfp710"
# convert human gene set collection to a list of gene symbols
gs_name <- hs_gs$gs_name
hs_gs_list <- hs_gs %>%
select(-c(collection, gs_name)) %>%
.$gene_symbol %>%
split(., gs_name)
hs_gs_list %>% head(.)
## $AAACCAC_MIR140
## [1] "ABCC4" "ABRAXAS2" "ACTN4" "ACVR1" "ADAM9" "ADAMTS5"
## [7] "AMER2" "ANK2" "API5" "ATOSA" "BACH1" "BAZ2B"
## [13] "BAZ2B" "BCL11A" "BCL2L2" "BCL9" "BMT2" "C1orf21"
## [19] "CACNA1C" "CEBPA" "CHD4" "CIT" "COL23A1" "CSK"
## [25] "CSNK1G3" "CTCF" "CUL3" "DAZL" "DBNDD2" "DCUN1D4"
## [31] "DDX3X" "DDX3Y" "DHX57" "DIPK2A" "DPP4" "DSCAM"
## [37] "DTNA" "E2F3" "EHD1" "EPHB1" "ERC2" "ETV3"
## [43] "EYA2" "GABARAP" "GALNT16" "GDF6" "GIT1" "GYS1"
## [49] "HDAC4" "HNRNPH3" "HSPA13" "IGFBP5" "KATNBL1" "KCND2"
## [55] "LOXL3" "LRRC4" "LRRC8E" "MAP3K8" "MDGA2" "MEX3C"
## [61] "MGAT1" "MMD" "MOK" "NAV3" "NKIRAS2" "NR3C1"
## [67] "NSD3" "NUTF2" "OGT" "OSTM1" "PDGFRA" "PFN1"
## [73] "PHF20L1" "PHYHIP" "PITX2" "PPP1CC" "PRIMA1" "R3HDM1"
## [79] "REEP1" "RNF19A" "RTKN2" "SENP1" "SIAH1" "SLC25A13"
## [85] "SLC38A2" "SLC41A2" "SLF2" "SLMAP" "SNX2" "SOX4"
## [91] "SRR" "STAG1" "STRADB" "SYT6" "TAF9B" "TBX3"
## [97] "TP53INP2" "TSHZ1" "TSPAN2" "TSSK2" "TTYH2" "UBASH3B"
## [103] "USP6" "VEGFA" "WNT1" "YES1" "ZBED4" "ZBTB10"
## [109] "ZNF182" "ZNF608" "ZNF654"
##
## $AAAGACA_MIR511
## [1] "ABCG8" "ACE" "ADAMTSL3" "ADGRF5" "ADSS2" "AGBL3"
## [7] "AGO1" "AGO2" "AGO4" "ALCAM" "ANAPC15" "ANKRD40CL"
## [13] "ANKZF1" "AQP6" "ARHGEF17" "ATL2" "ATP2B2" "ATRX"
## [19] "BCL11A" "BTG1" "BUB3" "C1QL2" "C1orf21" "CALM1"
## [25] "CAMK2N1" "CAMTA1" "CAPRIN1" "CCDC178" "CCND1" "CCNT2"
## [31] "CDH2" "CDK14" "CDK19" "CELF1" "CELF6" "CEP350"
## [37] "CFAP298" "CLK2" "CLTC" "CNOT4" "CORIN" "CREBRF"
## [43] "CREM" "CRIM1" "DCTN4" "DDX3X" "DDX3Y" "DEDD"
## [49] "DNAJB12" "DNAJC13" "DSC1" "DUSP6" "DYRK1B" "E2F3"
## [55] "EDEM3" "EFR3A" "ELAVL3" "EMILIN2" "EML4" "ENPP1"
## [61] "ENPP4" "EPHA4" "ESRRG" "EYA1" "EYA4" "FAM117A"
## [67] "FGF13" "FIP1L1" "FMR1" "FN1" "FNDC1" "FNDC5"
## [73] "FOXK2" "FOXN3" "GAD2" "GEMIN2" "GFAP" "GJA1"
## [79] "GLRA2" "HAS2" "HCN4" "HLF" "HLTF" "HOXA13"
## [85] "IGF2BP1" "IGF2BP3" "ILRUN" "KCNE1" "KCNMA1" "KHDRBS2"
## [91] "KLF9" "KLHL18" "KLHL24" "LATS1" "LMCD1" "LPP"
## [97] "LRCH4" "LUC7L3" "MAP3K2" "MAP4K4" "MAPK1IP1L" "MBD2"
## [103] "MBD6" "MDGA2" "METAP2" "MIB1" "MINK1" "MRPL21"
## [109] "MSTN" "MTAP" "MYCBP" "MYO19" "NAA50" "NACC1"
## [115] "NEUROD6" "NHLH2" "NLK" "NR4A2" "NRXN3" "NTRK2"
## [121] "NXPH1" "ONECUT2" "PAX8" "PCARE" "PCDH10" "PCDH17"
## [127] "PELI1" "PHAF1" "PHLPP1" "PIK3R3" "PMEPA1" "POGK"
## [133] "POU4F2" "PPARGC1A" "PRELP" "PRPF4B" "PSMA1" "PSMD10"
## [139] "PTGR3" "QKI" "RAB22A" "RAB2A" "RBM15B" "RBM26"
## [145] "RECK" "REV3L" "RGL1" "RHOJ" "RHOT1" "RNF19A"
## [151] "ROBO2" "RPS6KB1" "RPS6KL1" "SATB2" "SCN4B" "SELENOP"
## [157] "SEMA3F" "SEMA6D" "SINHCAF" "SLC22A17" "SLC25A26" "SLC6A6"
## [163] "SLITRK1" "SMARCE1" "SOCS2" "SORCS3" "SOST" "SOX12"
## [169] "SPTBN4" "SPTLC2" "SRGAP3" "SS18" "ST18" "SYT11"
## [175] "TAF5" "TBXT" "THOC5" "TIAL1" "TMEM196" "TMEM243"
## [181] "TMEM248" "TNRC6A" "TNRC6B" "TOB1" "TRAPPC3" "TRAPPC8"
## [187] "TRIM2" "TRIM24" "TSPOAP1" "TXNL1" "UBE2H" "VANGL2"
## [193] "VAV3" "VIRMA" "VKORC1L1" "VMP1" "WNT16" "YTHDF2"
## [199] "YY1" "ZCCHC24" "ZDHHC21" "ZNF319" "ZNF654" "ZNF706"
##
## $AAAGGAT_MIR501
## [1] "ACACA" "ACADSB" "ADCYAP1" "ADIPOR2" "ALS2" "ALX1"
## [7] "AMMECR1" "APOLD1" "ATP6V1H" "BCL6" "BCLAF1" "C8orf82"
## [13] "CACHD1" "CAMTA1" "CBLIF" "CCDC140" "CD164" "CDK2AP1"
## [19] "CELF2" "CELSR2" "CHODL" "CLK1" "CLK2" "CTDSP1"
## [25] "CTDSPL2" "CUL1" "CUX2" "DCX" "DNAJB12" "ELAVL4"
## [31] "ERRFI1" "GRB10" "H2AX" "HAS2" "HES5" "HOXB8"
## [37] "JADE3" "JUN" "KCND2" "KCNRG" "KIF1C" "KIF2A"
## [43] "KLHL14" "KRR1" "LARP1" "LEPROTL1" "LPGAT1" "LPIN1"
## [49] "LRRC1" "MAP2K1" "MAP3K8" "MCU" "MEF2C" "MYB"
## [55] "MYCL" "MYLK" "NEXMIF" "NFASC" "NFIL3" "NFIX"
## [61] "NPR3" "NR2F2" "NR4A3" "PCDH19" "PDK1" "PHC1"
## [67] "PHF6" "PIK3AP1" "PITX2" "PLP1" "PLXNB1" "PNN"
## [73] "PPP1CB" "PPP2R5E" "PPP4R3A" "PPP6R3" "PRKCE" "PURA"
## [79] "QKI" "RAB22A" "RABGEF1" "RASL10B" "RCN1" "RDX"
## [85] "RET" "RGL1" "RNF11" "ROBO2" "RPGRIP1L" "RSBN1"
## [91] "SATB2" "SCN3A" "SENP3" "SEPHS1" "SGPP1" "SLC25A3"
## [97] "SLC35B3" "SLITRK5" "SMC1A" "SNAP29" "SOX11" "SOX4"
## [103] "SPOPL" "SRR" "SRSF2" "SYNC" "SYNJ1" "SYT7"
## [109] "TAF5L" "TAPT1" "TNNI2" "TOGARAM1" "TOMM70" "TRIM39"
## [115] "TSC22D3" "UBAP1" "UBE2Q1" "UBE4B" "USP12" "VDAC2"
## [121] "WDFY3" "WIPF2" "WT1-AS" "ZBTB18" "ZC3H7A" "ZIC4"
## [127] "ZMYM5"
##
## $AAAGGGA_MIR204_MIR211
## [1] "ABRAXAS2" "ADAMTS9" "ADCY6" "ADPRM" "AGO4" "AKAP1"
## [7] "ALPL" "ANGPT1" "ANKRD13A" "ANXA11" "AP1S1" "AP1S3"
## [13] "AP2A2" "AP3M1" "APH1A" "ARAP2" "ARCN1" "ARGLU1"
## [19] "ARHGAP29" "ARL8B" "ATF2" "ATP2B1" "AUP1" "BAZ2A"
## [25] "BCL11B" "BCL2" "BCL9" "BCL9L" "BRD4" "BRPF3"
## [31] "CAPRIN1" "CCDC120" "CCNT2" "CCPG1" "CDC25B" "CDC42"
## [37] "CDH2" "CELSR3" "CHD5" "CHN2" "CHP1" "CLIP1"
## [43] "CORO1C" "COX5A" "CPD" "CPNE8" "CREB5" "CRKL"
## [49] "CTDNEP1" "DAG1" "DCAF5" "DCUN1D3" "DENND5A" "DHH"
## [55] "DLG5" "DMTF1" "DNAJC13" "DNM2" "DTX1" "DVL3"
## [61] "DYRK1A" "EDEM1" "EEF1E1" "EFNB3" "ELAVL3" "ELF2"
## [67] "ELL2" "ELMOD3" "ELOVL6" "EPHA7" "EPHB6" "ESR1"
## [73] "ESRRG" "EVA1C" "EZR" "FAM117B" "FAM120C" "FARP1"
## [79] "FBN2" "FBXW7" "FHIP1B" "FJX1" "FNIP1" "FRAS1"
## [85] "FREM1" "FRY" "GABRB3" "GAPVD1" "GGA2" "GLIS3"
## [91] "GPM6A" "GRM1" "HAPSTR1" "HIC2" "HMGA2" "HOOK3"
## [97] "HOXC8" "HS2ST1" "IGF2R" "ING4" "ITPR1" "JPH3"
## [103] "KCNA3" "KCTD1" "KDM2A" "KHDRBS1" "KHDRBS3" "KITLG"
## [109] "KLF12" "KLHL13" "KMT2A" "KMT5A" "LATS1" "LPAR1"
## [115] "LRRC8D" "MALL" "MAML3" "MAP1LC3B" "MAP3K3" "MBNL1"
## [121] "MED13L" "METAP1" "MIR600HG" "MLLT3" "MMGT1" "MON2"
## [127] "MRPL35" "MRPL52" "MYO10" "NAA15" "NBEA" "NCOA7"
## [133] "NEUROG1" "NOVA1" "NPTX1" "NR3C1" "NR4A2" "NRBF2"
## [139] "NTRK2" "P4HB" "PABIR2" "PCDH9" "PHF13" "PID1"
## [145] "PLAG1" "POU3F2" "PPARGC1A" "PPP3R1" "PRDM2" "PRPF38B"
## [151] "PRRX1" "RAB10" "RAB14" "RAB1A" "RAP2C" "RBSN"
## [157] "REEP1" "RERE" "RHOBTB3" "RHOT1" "RICTOR" "RPS6KA3"
## [163] "RPS6KA5" "RPS6KC1" "RSPO3" "RTKN2" "RUNX2" "SATB2"
## [169] "SCRT2" "SEC24D" "SEC61A2" "SERINC3" "SF3B1" "SGCZ"
## [175] "SGIP1" "SHC1" "SIN3A" "SIRT1" "SLC17A7" "SLC22A2"
## [181] "SLC37A3" "SLITRK4" "SLTM" "SMOC1" "SOCS6" "SOX11"
## [187] "SOX4" "SPOP" "SPRED1" "SPRYD7" "SSRP1" "ST7"
## [193] "STXBP5" "SUMO2" "SUMO4" "SZRD1" "TAF5" "TCF12"
## [199] "TCF7L1" "TGFBR2" "TMEM30A" "TMOD3" "TNRC6B" "TP53INP1"
## [205] "TRIAP1" "TRIP12" "TRPC5" "TTYH1" "UBE2R2" "UHRF2"
## [211] "USP6" "WEE1" "WNT4" "WSB1" "XRN1" "YTHDF3"
## [217] "YWHAG" "ZCCHC14" "ZCCHC24" "ZDHHC17" "ZFC3H1" "ZFP91"
## [223] "ZNF282" "ZNF335" "ZNF423"
##
## $AAANWWTGC_UNKNOWN
## [1] "ACTB" "ADHFE1" "AFF4" "ANK2" "ANK3" "APP"
## [7] "ASPA" "ATOH7" "ATP1B1" "ATP2B4" "ATXN7L1" "BCL11A"
## [13] "BCL6" "BNC2" "C11orf87" "CACNA1D" "CACNG3" "CALM1"
## [19] "CD14" "CDC42EP3" "CDC42EP5" "CDH13" "CDK2AP1" "CEPT1"
## [25] "CHD2" "CITED2" "CNMD" "CNTFR" "DAB1" "DCAF11"
## [31] "DCHS2" "DDIT3" "DIS3L" "DLG2" "DLGAP4" "DMD"
## [37] "DNAJB5" "DPYSL5" "DRD3" "DSCAM" "DSEL" "DSTN"
## [43] "DTX3L" "DUSP1" "DYNC1I2" "EBF1" "EFNA5" "EGFLAM"
## [49] "EIF4EBP2" "ELAVL4" "ELF4" "EPHA7" "EPHB2" "ESR1"
## [55] "FAM78A" "FBXW7" "FGF7" "FGFR2" "FN1" "FOXN3"
## [61] "FOXP1" "FOXP2" "FTHL17" "FZD7" "GANAB" "GATA3"
## [67] "GLRA2" "GPC3" "GPC6" "GPR21" "GPRIN3" "GRHL3"
## [73] "GRIN2B" "GTF2E2" "HEPACAM" "HHEX" "HOXA2" "HOXA3"
## [79] "HOXB2" "HOXB6" "HOXC4" "IGF2BP1" "INHBA" "ITM2C"
## [85] "JADE2" "KANK1" "KCNJ13" "KLF12" "KLF14" "KRTAP8-1"
## [91] "LEAP2" "LINC00314" "LIPG" "LOX" "LOXL4" "LRRC3B"
## [97] "LRRN1" "LSAMP" "LUC7L3" "MAML3" "MAN2A2" "MAP3K4"
## [103] "MAPK3" "MBNL1" "MEF2C" "MEIS1" "MGLL" "MID1"
## [109] "MLLT6" "MMP3" "MPZL3" "MRAP" "MRPL24" "MRPS18B"
## [115] "MYCL" "MYH2" "MYLK" "NCBP3" "NEK6" "NEUROG1"
## [121] "NFE2L2" "NNAT" "NR2F2" "NRAS" "NTN1" "NTRK3"
## [127] "OLFM1" "OLIG2" "OMG" "OTX2" "PARP9" "PATZ1"
## [133] "PAX1" "PAX6" "PCSK1" "PCTP" "PDGFRB" "PHOX2B"
## [139] "PHTF1" "PIK3R3" "POU2F1" "POU4F1" "PPARGC1A" "PPFIA2"
## [145] "PPP1R10" "PPP2R2A" "PPP3CC" "PRDM16" "PRIMA1" "PRPF4B"
## [151] "RAB10" "RBMX" "RORA" "RRS1" "RSPO2" "S100PBP"
## [157] "SALL3" "SAMD12" "SATB2" "SEMA6C" "SESN2" "SFRP2"
## [163] "SGCD" "SHC3" "SIX5" "SKIL" "SKP2" "SLMAP"
## [169] "SNCAIP" "SNX25" "SORT1" "SOX13" "SOX4" "SOX5"
## [175] "SPAG9" "SPARCL1" "SSBP3" "STEAP2" "TBC1D8B" "TFAP4"
## [181] "TFDP2" "TGIF1" "THAP12" "THBS2" "TLE4" "TLK1"
## [187] "TLX3" "TRAM1" "TRPM3" "TSC22D4" "ZFPM1" "ZHX3"
## [193] "ZNF462" "ZNF827" "ZW10"
##
## $AAAYRNCTG_UNKNOWN
## [1] "ABT1" "ACVR1" "ADAM12" "ADD3" "ADGRB3" "AGGF1"
## [7] "ANKRD12" "ANKRD28" "AP4S1" "APBB2" "APOBR" "AQP2"
## [13] "ARHGAP44" "ARID1A" "ARID4A" "ARPC2" "ARSG" "ARX"
## [19] "ASB4" "ASPH" "ATOH8" "ATP1A2" "ATP5IF1" "ATP5MG"
## [25] "AXDND1" "B4GALT6" "BAMBI" "BCL2L1" "BCL9" "BMPR1B"
## [31] "BMX" "BRSK2" "BTBD3" "BUB3" "C7orf33" "CA3"
## [37] "CACNA2D3" "CACNB2" "CAPN1" "CAPZA1" "CASQ2" "CBX2"
## [43] "CCDC174" "CCNJ" "CCNY" "CDC23" "CDH2" "CER1"
## [49] "CFAP161" "CHRM1" "CITED2" "CLDN5" "CLTC" "CLTRN"
## [55] "CMKLR1" "CNTLN" "CNTN1" "COCH" "COL12A1" "COL1A2"
## [61] "COL4A5" "COL4A6" "COLCA1" "COLEC10" "CRAT" "CRH"
## [67] "CRKL" "CRYGD" "CRYGS" "CSNK1A1" "CSRNP3" "CSTF3"
## [73] "CYBRD1" "CYRIA" "DAAM1" "DBNDD2" "DCAKD" "DDAH2"
## [79] "DDX4" "DEF6" "DENND4A" "DGKB" "DHH" "DHRS4"
## [85] "DHRS4L2" "DIDO1" "DMD" "DMRT1" "DNAJA2" "DNAJB3"
## [91] "DNAJB3" "DNAJB4" "DSCAML1" "DUSP4" "DYNC1I1" "DYRK1A"
## [97] "EDA" "EFNA1" "EGFLAM" "EIF5" "EMX2" "EPC1"
## [103] "EPHA7" "ERBB4" "ERG28" "ERRFI1" "ESRP2" "ESRRB"
## [109] "ESRRG" "EYA1" "FAM216B" "FAM83F" "FCER1A" "FGD4"
## [115] "FGF10" "FGF12" "FGFR1" "FGFR1OP2" "FIZ1" "FKRP"
## [121] "FMNL3" "FNDC9" "FOXA1" "FOXG1" "FOXO4" "FOXP2"
## [127] "FSIP2" "FST" "GABRA3" "GDNF" "GFI1" "GGNBP2"
## [133] "GJB4" "GLDN" "GNAQ" "GPR85" "GPRC5D" "GRIN2B"
## [139] "GSE1" "H3-3A" "HDAC8" "HESX1" "HEXIM2" "HGF"
## [145] "HIC2" "HID1" "HIP1R" "HOXA10" "HOXA5" "HOXB8"
## [151] "HPSE2" "HSD3B7" "ICAM4" "ID1" "IGF1" "IL1RAPL1"
## [157] "INHBC" "IP6K2" "ITGA10" "ITGA8" "JADE2" "JPH1"
## [163] "JPT1" "KANK2" "KCNIP2" "KCNK5" "KCNN3" "KCNQ1DN"
## [169] "KITLG" "KLF5" "KLHDC10" "KLHL20" "KLHL3" "KMT2A"
## [175] "LARS2" "LBX2-AS1" "LENG9" "LHFPL6" "LHX9" "LINC02910"
## [181] "LIX1" "LMO7" "LRP5" "LRRC4" "LRRN4CL" "LTBP1"
## [187] "MAML1" "MANF" "MAP2" "MAP3K5" "MAP6" "MEIS1"
## [193] "MGAT1" "MGAT4A" "MID1" "MOAP1" "MPPED2" "MRPL13"
## [199] "MTA2" "MTBP" "MTRFR" "MYF6" "MYH1" "MYH10"
## [205] "MYO18A" "NAGLU" "NAPB" "NAV2" "NAV3" "NCDN"
## [211] "NDNF" "NDST4" "NDUFS4" "NEK1" "NEK2" "NFATC4"
## [217] "NFYB" "NMI" "NMT1" "NR2F1" "NRG1" "NTRK2"
## [223] "NUP54" "NXPH4" "OMA1" "OMG" "OR2L13" "OTX2"
## [229] "PACRG" "PALS2" "PART1" "PCDH17" "PCDH18" "PCF11"
## [235] "PCYT1B" "PDGFB" "PDGFRA" "PDLIM2" "PDS5B" "PDZRN4"
## [241] "PFN2" "PHC2" "PHEX" "PHF1" "PHF6" "PHOX2B"
## [247] "PLAGL2" "PLEC" "PLEKHM1" "PLP2" "PLPP3" "PMCH"
## [253] "PMCHL1" "PODXL2" "POFUT1" "POU2AF1" "POU4F1" "PPP1R9B"
## [259] "PPP2R3A" "PPP2R5E" "PPP3CA" "PRELP" "PRKCG" "PRKCQ"
## [265] "PRKN" "PROK2" "PTCHD4" "PTGR3" "PTH1R" "PTPA"
## [271] "PXN" "R3HDM1" "RAB30" "RAB5B" "RAB5C" "RAPGEF4"
## [277] "RBMS3" "RGS17" "RNF146" "ROBO4" "ROR1" "RPLP0"
## [283] "RTN1" "S1PR2" "SCN3B" "SCN5A" "SCN8A" "SCOC"
## [289] "SDCBP" "SEMA6D" "SEPTIN7" "SESN3" "SGCD" "SH2D6"
## [295] "SHC3" "SHCBP1L" "SIPA1" "SIRPA" "SLC26A6" "SLC4A1"
## [301] "SLC6A1" "SMARCA2" "SNX9" "SORBS2" "SOX12" "SOX21"
## [307] "SOX30" "SOX5" "SPINDOC" "SPOCK2" "SPTLC2" "SRGAP2"
## [313] "SRSF8" "SSBP2" "ST7L" "STAC3" "STAG1" "STAG2"
## [319] "STC2" "STRN3" "STRN4" "TAS1R2" "TEF" "TENT4B"
## [325] "TFAP4" "TFDP2" "TM2D3" "TMEM182" "TMEM69" "TMSB4X"
## [331] "TMSB4XP1" "TMSB4XP6" "TMSB4XP8" "TNFAIP8" "TNS1" "TNXB"
## [337] "TP53INP2" "TRDN" "TREML1" "TRIM28" "TRIM68" "TRIM8"
## [343] "TRIML1" "TRPS1" "TSC22D3" "TSPAN7" "TSPY26P" "TSSK3"
## [349] "TTC17" "TUSC2" "UBE2W" "UBXN10" "USP1" "VDR"
## [355] "VIP" "VKORC1L1" "VWA5A" "WBP1" "WNT2B" "WT1"
## [361] "WT1-AS" "XRCC1" "ZBTB11" "ZBTB18" "ZFP91" "ZFPM2"
## [367] "ZIC1" "ZIC4" "ZMAT3" "ZNF296" "ZNF503" "ZNF521"
## [373] "ZNF524" "ZNF654" "ZNF687" "ZNF710"
# create GMT files for mouse and human gene set collections
write.gmt <- function(genelist, file) {
file_conn <- file(file, open = "wt")
for (set_name in names(genelist)) {
line <- c(set_name, set_name, genelist[[set_name]])
writeLines(paste(line, collapse = "\t"), file_conn)}
close(file_conn)}
# Save GMT files to temporary directory
write.gmt(mm_gs_list, file.path(temp_dir, "20250319_mouse_msgidbr.gmt"))
write.gmt(hs_gs_list, file.path(temp_dir, "20250319_human_msgidbr.gmt"))