genes.by.gobp.pathway
genes.by.gobp.pathway.RdA go term bp gene set from
x <- readLines("c5.go.bp.v7.5.1.symbols.gmt")
res <- strsplit(x, "\t")
names(res) <- vapply(res, function(y) y[1], character(1))
genes.by.gobp.pathway <- lapply(res, "[", -c(1:2))
Usage
data(genes.by.gobp.pathway)Examples
data(genes.by.gobp.pathway)
str(genes.by.gobp.pathway)
#> List of 7658
#> $ GOBP_MITOCHONDRIAL_GENOME_MAINTENANCE : chr [1:23] "AKT3" "PPARGC1A" "POLG2" "PARP1" ...
#> $ GOBP_REPRODUCTION : chr [1:1514] "ADA" "GNPDA1" "ZGLP1" "TDRD15" ...
#> $ GOBP_SINGLE_STRAND_BREAK_REPAIR : chr [1:12] "ENSG00000254469" "ERCC8" "PARP1" "APLF" ...
#> $ GOBP_REGULATION_OF_DNA_RECOMBINATION : chr [1:131] "PARP3" "ACTR2" "RAD50" "ALYREF" ...
#> $ GOBP_REGULATION_OF_MITOTIC_RECOMBINATION : chr [1:7] "RAD50" "ANKLE1" "ZSCAN4" "ERCC2" ...
#> $ GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY : chr [1:27] "RPL10L" "RPLP0P6" "FASTKD2" "DHX30" ...
#> $ GOBP_RIBOSOMAL_SMALL_SUBUNIT_ASSEMBLY : chr [1:19] "ENSG00000275464" "ERAL1" "RRP7A" "ABT1" ...
#> $ GOBP_VERY_LONG_CHAIN_FATTY_ACID_METABOLIC_PROCESS : chr [1:35] "ACOT2" "SLC27A5" "SLC27A4" "SLC27A2" ...
#> $ GOBP_TRANSITION_METAL_ION_TRANSPORT : chr [1:105] "ABCC5" "ABCB6" "COX17" "PGRMC2" ...
#> $ GOBP_UREA_CYCLE : chr [1:10] "SLC25A15" "CEBPA" "CPS1" "NAGS" ...
#> $ GOBP_CITRULLINE_METABOLIC_PROCESS : chr [1:8] "CPS1" "DDAH2" "DDAH1" "ASS1" ...
#> $ GOBP_RIBOSOMAL_SUBUNIT_EXPORT_FROM_NUCLEUS : chr [1:14] "NOP9" "RRS1" "EIF6" "NPM1" ...
#> $ GOBP_RIBOSOMAL_LARGE_SUBUNIT_EXPORT_FROM_NUCLEUS : chr [1:7] "RRS1" "NPM1" "NUP88" "NMD3" ...
#> $ GOBP_RIBOSOMAL_SMALL_SUBUNIT_EXPORT_FROM_NUCLEUS : chr [1:8] "NOP9" "NPM1" "NUP88" "RIOK2" ...
#> $ GOBP_MITOTIC_SISTER_CHROMATID_SEGREGATION : chr [1:173] "UBE2DNL" "PDCD6IP" "SMC4" "AKAP8" ...
#> $ GOBP_CELL_CYCLE_CHECKPOINT_SIGNALING : chr [1:170] "FEM1B" "CDK2" "CDKN1A" "CDKN1B" ...
#> $ GOBP_DNA_REPLICATION_CHECKPOINT_SIGNALING : chr [1:17] "TOPBP1" "HUS1B" "RAD9B" "DNA2" ...
#> $ GOBP_REGULATION_OF_TRANSCRIPTION_INVOLVED_IN_G1_S_TRANSITION_OF_MITOTIC_CELL_CYCLE : chr [1:21] "CDK5" "E2F7" "E2F1" "E2F4" ...
#> $ GOBP_SULFUR_AMINO_ACID_METABOLIC_PROCESS : chr [1:33] "CBSL" "CDO1" "CPS1" "CTH" ...
#> $ GOBP_SULFUR_AMINO_ACID_BIOSYNTHETIC_PROCESS : chr [1:17] "CBSL" "CDO1" "CTH" "BHMT2" ...
#> $ GOBP_SULFUR_AMINO_ACID_CATABOLIC_PROCESS : chr [1:10] "CBSL" "CDO1" "AGXT" "MAT1A" ...
#> $ GOBP_SULFUR_AMINO_ACID_TRANSPORT : chr [1:9] "SLC7A9" "MFSD12" "CTNS" "SLC7A13" ...
#> $ GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II : chr [1:931] "NR2E3" "ZBTB33" "ZGLP1" "ZBTB42" ...
#> $ GOBP_RRNA_MODIFICATION : chr [1:37] "METTL15P1" "EMG1" "RPUSD1" "BUD23" ...
#> $ GOBP_MAPK_CASCADE : chr [1:792] "CDH2" "CD24" "SH2B3" "SH2D3C" ...
#> $ GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_NONSENSE_MEDIATED_DECAY : chr [1:40] "RNPS1" "PNLDC1" "DCP2" "DCP1B" ...
#> $ GOBP_PROTEIN_POLYUBIQUITINATION : chr [1:244] "HDAC6" "UBE2DNL" "HUWE1" "RNF41" ...
#> $ GOBP_MEIOTIC_SPINDLE_ORGANIZATION : chr [1:15] "NDC80" "ASPM" "FBXO5" "TUBG2" ...
#> $ GOBP_MICROTUBULE_CYTOSKELETON_ORGANIZATION : chr [1:642] "HDAC6" "GOLGA8DP" "PDCD6IP" "CDH5" ...
#> $ GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY : chr [1:25] "RNU4ATAC" "RNU6ATAC" "RNU6-9" "RNU6-7" ...
#> $ GOBP_SPLICEOSOMAL_COMPLEX_ASSEMBLY : chr [1:77] "RNU4ATAC" "RNU6ATAC" "RNVU1-8" "RBM5" ...
#> $ GOBP_ALLANTOIN_METABOLIC_PROCESS : chr [1:8] "ADA" "NT5C2" "NT5C" "PNP" ...
#> $ GOBP_MITOCHONDRIAL_FISSION : chr [1:40] "DNM1L" "RALBP1" "MTFR2" "LRRK2" ...
#> $ GOBP_PEPTIDOGLYCAN_METABOLIC_PROCESS : chr [1:6] "PGLYRP2" "PGLYRP3" "LYG1" "LYG2" ...
#> $ GOBP_POLYSACCHARIDE_BIOSYNTHETIC_PROCESS : chr [1:75] "MIR1271" "B3GNT3" "SORBS1" "B3GNT2" ...
#> $ GOBP_POLYSACCHARIDE_CATABOLIC_PROCESS : chr [1:19] "CHIT1" "AGL" "G6PC1" "GAA" ...
#> $ GOBP_MITOTIC_CELL_CYCLE : chr [1:900] "SRA1" "MIR892B" "UBE2DNL" "PDCD6IP" ...
#> $ GOBP_MITOTIC_CYTOKINESIS : chr [1:71] "PDCD6IP" "KIF20A" "CENPA" "STAMBP" ...
#> $ GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_DEADENYLATION_DEPENDENT_DECAY : chr [1:63] "TOB1" "SYNCRIP" "PAIP1" "IGF2BP1" ...
#> $ GOBP_NUCLEAR_TRANSCRIBED_MRNA_POLY_A_TAIL_SHORTENING : chr [1:28] "TOB1" "TENT4A" "PNLDC1" "CPEB3" ...
#> $ GOBP_DEADENYLATION_DEPENDENT_DECAPPING_OF_NUCLEAR_TRANSCRIBED_MRNA : chr [1:10] "DCP2" "DCP1B" "PATL2" "PATL1" ...
#> $ GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_EXONUCLEOLYTIC : chr [1:19] "EXOSC8" "NT5C3B" "EXOSC6" "DIS3L2" ...
#> $ GOBP_RETROGRADE_TRANSPORT_VESICLE_RECYCLING_WITHIN_GOLGI : chr [1:9] "COG5" "COG2" "COG4" "COG6" ...
#> $ GOBP_RESPONSE_TO_REACTIVE_OXYGEN_SPECIES : chr [1:204] "MIR675" "HDAC6" "IL18BP" "PPIF" ...
#> $ GOBP_RESPONSE_TO_OXYGEN_RADICAL : chr [1:29] "MIR675" "FBLN5" "TXNRD2" "DHFR" ...
#> $ GOBP_PROTEIN_DENEDDYLATION : chr [1:10] "COPS8" "COPS6" "COPS5" "TOR1A" ...
#> $ GOBP_FORMATION_OF_QUADRUPLE_SL_U4_U5_U6_SNRNP : chr [1:10] "RNU6-9" "RNU6-7" "RNU6-1" "RNU5F-1" ...
#> $ GOBP_RNA_SPLICING_VIA_TRANSESTERIFICATION_REACTIONS : chr [1:322] "SNRPGP15" "RNU4ATAC" "RNU6ATAC" "PQBP1" ...
#> $ GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME : chr [1:77] "PQBP1" "MBNL2" "RBM7" "RBM5" ...
#> $ GOBP_REGULATION_OF_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME : chr [1:60] "MBNL2" "RBM7" "RBM5" "SAP18" ...
#> $ GOBP_SPLICEOSOMAL_SNRNP_ASSEMBLY : chr [1:50] "SNRPGP15" "RNU4ATAC" "RNU6ATAC" "RNU6-9" ...
#> $ GOBP_MRNA_3_SPLICE_SITE_RECOGNITION : chr [1:6] "SF3A1" "SLU7" "SF3A3" "ISY1" ...
#> $ GOBP_SPLICEOSOMAL_CONFORMATIONAL_CHANGES_TO_GENERATE_CATALYTIC_CONFORMATION : chr [1:5] "SNRNP200" "YJU2" "XAB2" "ISY1" ...
#> $ GOBP_RNA_SPLICING_VIA_ENDONUCLEOLYTIC_CLEAVAGE_AND_LIGATION : chr [1:11] "CLP1" "TSEN15" "DDX1" "ERN1" ...
#> $ GOBP_MRNA_5_SPLICE_SITE_RECOGNITION : chr [1:23] "RNU4ATAC" "RNU6ATAC" "RNVU1-8" "RNVU1-4" ...
#> $ GOBP_PROTEIN_PEPTIDYL_PROLYL_ISOMERIZATION : chr [1:42] "PPIF" "CWC27" "PPIE" "PPIH" ...
#> $ GOBP_REGULATION_OF_HISTONE_H3_K36_METHYLATION : chr [1:7] "PAXIP1" "BRD4" "BCOR" "NSD3" ...
#> $ GOBP_AUTOPHAGY_OF_MITOCHONDRION : chr [1:88] "HDAC6" "DNM1L" "HUWE1" "OPTN" ...
#> $ GOBP_MITOPHAGY : chr [1:34] "HDAC6" "HUWE1" "OPTN" "RNF41" ...
#> $ GOBP_ENDONUCLEOLYTIC_CLEAVAGE_IN_ITS1_TO_SEPARATE_SSU_RRNA_FROM_5_8S_RRNA_AND_LSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA: chr [1:9] "RCL1" "RPP40" "NOP9" "RRS1" ...
#> $ GOBP_ENZYME_DIRECTED_RRNA_PSEUDOURIDINE_SYNTHESIS : chr [1:6] "RPUSD1" "TSR3" "DKC1" "RPUSD2" ...
#> $ GOBP_MATURATION_OF_5_8S_RRNA : chr [1:35] "RCL1" "MPHOSPH6" "NSA2" "C1D" ...
#> $ GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA : chr [1:37] "RCL1" "ENSG00000275464" "TBL3" "RPP40" ...
#> $ GOBP_MATURATION_OF_LSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA : chr [1:15] "RPL35" "FTSJ3" "BOP1" "PES1" ...
#> $ GOBP_MATURATION_OF_5_8S_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA : chr [1:24] "RCL1" "RPP40" "ERI2" "EXOSC8" ...
#> $ GOBP_CLEAVAGE_INVOLVED_IN_RRNA_PROCESSING : chr [1:27] "RCL1" "TBL3" "RPP40" "ERI2" ...
#> $ GOBP_MATURATION_OF_LSU_RRNA : chr [1:28] "NSA2" "RPL35" "FTSJ3" "BOP1" ...
#> $ GOBP_ENDONUCLEOLYTIC_CLEAVAGE_INVOLVED_IN_RRNA_PROCESSING : chr [1:15] "RCL1" "TBL3" "RPP40" "NOP9" ...
#> $ GOBP_ENDONUCLEOLYTIC_CLEAVAGE_IN_5_ETS_OF_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA : chr [1:7] "RCL1" "TBL3" "NOP9" "UTP20" ...
#> $ GOBP_SMALL_NUCLEOLAR_RIBONUCLEOPROTEIN_COMPLEX_ASSEMBLY : chr [1:12] "RUVBL2" "PIH1D2" "NOPCHAP1" "NUFIP1" ...
#> $ GOBP_BOX_C_D_SNORNP_ASSEMBLY : chr [1:10] "RUVBL2" "PIH1D2" "NOPCHAP1" "NUFIP1" ...
#> $ GOBP_EMBRYONIC_AXIS_SPECIFICATION : chr [1:43] "TDRD15" "BASP1" "FRS2" "TMED2" ...
#> $ GOBP_RESOLUTION_OF_MEIOTIC_RECOMBINATION_INTERMEDIATES : chr [1:17] "CORT" "EME1" "SHOC1" "HFM1" ...
#> $ GOBP_TELOMERE_MAINTENANCE_VIA_RECOMBINATION : chr [1:15] "RAD50" "ERCC1" "ERCC4" "SMC5" ...
#> $ GOBP_TELOMERE_MAINTENANCE : chr [1:132] "TEN1" "PARP3" "RAD50" "CCT7" ...
#> $ GOBP_RECOMBINATIONAL_REPAIR : chr [1:164] "ACTR2" "PSMD14" "MAD2L2" "KAT5" ...
#> $ GOBP_DOUBLE_STRAND_BREAK_REPAIR_VIA_BREAK_INDUCED_REPLICATION : chr [1:12] "MCMDC2" "MCM2" "MCM3" "MCM4" ...
#> $ GOBP_DNA_DOUBLE_STRAND_BREAK_PROCESSING : chr [1:19] "DNA2" "SPO11" "C14orf39" "MRE11" ...
#> $ GOBP_DNA_SYNTHESIS_INVOLVED_IN_DNA_REPAIR : chr [1:37] "CDKN2D" "MAD2L2" "POLD3" "POLI" ...
#> $ GOBP_DNA_CATABOLIC_PROCESS_ENDONUCLEOLYTIC : chr [1:26] "CIDEA" "DFFA" "DFFB" "DNASE1" ...
#> $ GOBP_DNA_CATABOLIC_PROCESS_EXONUCLEOLYTIC : chr [1:5] "TREX2" "TREX1" "XRN2" "ISG20" ...
#> $ GOBP_SISTER_CHROMATID_SEGREGATION : chr [1:207] "UBE2DNL" "PDCD6IP" "DDX11L8" "SMC4" ...
#> $ GOBP_REGULATION_OF_GLUTAMINE_FAMILY_AMINO_ACID_METABOLIC_PROCESS : chr [1:8] "CLN3" "SIRT4" "SLC7A11" "MIR21" ...
#> $ GOBP_CELL_MORPHOGENESIS : chr [1:1004] "CDH2" "ABI1" "GJE1" "HDAC6" ...
#> $ GOBP_CELL_MORPHOGENESIS_INVOLVED_IN_DIFFERENTIATION : chr [1:711] "CDH2" "ABI1" "HDAC6" "CDH4" ...
#> $ GOBP_CYTOKINESIS : chr [1:174] "PDCD6IP" "ACTR3" "ACTR2" "KIF20A" ...
#> $ GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS : chr [1:123] "TOB1" "SYNCRIP" "PAIP1" "IGF2BP1" ...
#> $ GOBP_MITOCHONDRIAL_RNA_CATABOLIC_PROCESS : chr [1:6] "LRPPRC" "PDE12" "GRSF1" "SUPV3L1" ...
#> $ GOBP_MITOCHONDRIAL_RNA_METABOLIC_PROCESS : chr [1:49] "LRPPRC" "WARS2" "FASTK" "EARS2" ...
#> $ GOBP_REGULATION_OF_MITOCHONDRIAL_RNA_CATABOLIC_PROCESS : chr [1:5] "LRPPRC" "GRSF1" "SUPV3L1" "SLIRP" ...
#> $ GOBP_MITOCHONDRIAL_RNA_PROCESSING : chr [1:20] "FASTK" "FASTKD2" "MTO1" "HSD17B10" ...
#> $ GOBP_MITOCHONDRIAL_RNA_3_END_PROCESSING : chr [1:5] "HSD17B10" "TRNT1" "TRMT10C" "SUPV3L1" ...
#> $ GOBP_RNA_5_END_PROCESSING : chr [1:23] "POP7" "RPP30" "RPP38" "TBL3" ...
#> $ GOBP_RRNA_5_END_PROCESSING : chr [1:5] "TBL3" "NOP9" "UTP20" "ABT1" ...
#> $ GOBP_TRANSCRIPTION_DEPENDENT_TETHERING_OF_RNA_POLYMERASE_II_GENE_DNA_AT_NUCLEAR_PERIPHERY : chr [1:6] "NUP133" "PCID2" "NUP107" "RAE1" ...
#> $ GOBP_RESPONSE_TO_ACID_CHEMICAL : chr [1:129] "CDKN1B" "RRAGB" "CDO1" "KLF2" ...
#> $ GOBP_RNA_POLYMERASE_I_PREINITIATION_COMPLEX_ASSEMBLY : chr [1:9] "BAZ2A" "RRN3" "PIH1D1" "POLR1E" ...
#> $ GOBP_FORMATION_OF_EXTRACHROMOSOMAL_CIRCULAR_DNA : chr [1:15] "DNA2" "ERCC1" "NBN" "SMARCAL1" ...
#> $ GOBP_GUANINE_NUCLEOTIDE_TRANSPORT : chr [1:8] "ABCC5" "ABCC4" "LRRC8D" "LRRC8A" ...
#> [list output truncated]