genes.by.reactome.pathway
genes.by.reactome.pathway.RdA celltype pathway gene set from
x <- readLines("c2.cp.reactome.v7.5.1.symbols.gmt")
res <- strsplit(x, "\t")
names(res) <- vapply(res, function(y) y[1], character(1))
genes.by.reactome.pathway <- lapply(res, "[", -c(1:2))
save(genes.by.reactome.pathway,file = "genes.by.reactome.pathway.RData")
Usage
data(genes.by.reactome.pathway)Examples
data(genes.by.reactome.pathway)
str(genes.by.reactome.pathway)
#> List of 1615
#> $ REACTOME_INTERLEUKIN_6_SIGNALING : chr [1:11] "JAK2" "TYK2" "CBL" "STAT1" ...
#> $ REACTOME_APOPTOSIS : chr [1:179] "BAD" "CFLAR" "PSMB1" "PSMC4" ...
#> $ REACTOME_HEMOSTASIS : chr [1:678] "FGR" "CD99" "TFPI" "KDM1A" ...
#> $ REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS : chr [1:55] "BAD" "BID" "BAK1" "CASP8" ...
#> $ REACTOME_MAPK3_ERK1_ACTIVATION : chr [1:10] "JAK2" "MAPK3" "TYK2" "IL6ST" ...
#> $ REACTOME_TRANSLESION_SYNTHESIS_BY_Y_FAMILY_DNA_POLYMERASES_BYPASSES_LESIONS_ON_DNA_TEMPLATE : chr [1:39] "REV3L" "SPRTN" "RFC1" "RFC2" ...
#> $ REACTOME_RECOGNITION_OF_DNA_DAMAGE_BY_PCNA_CONTAINING_REPLICATION_COMPLEX : chr [1:30] "RFC1" "RFC2" "POLD1" "RAD18" ...
#> $ REACTOME_TRANSLESION_SYNTHESIS_BY_POLH : chr [1:19] "SPRTN" "RFC1" "RFC2" "UFD1" ...
#> $ REACTOME_RECOGNITION_AND_ASSOCIATION_OF_DNA_GLYCOSYLASE_WITH_SITE_CONTAINING_AN_AFFECTED_PURINE : chr [1:54] "TINF2" "ACD" "MPG" "H2AZ2" ...
#> $ REACTOME_DISPLACEMENT_OF_DNA_GLYCOSYLASE_BY_APEX1 : chr [1:9] "NTHL1" "UNG" "APEX1" "MPG" ...
#> $ REACTOME_POLB_DEPENDENT_LONG_PATCH_BASE_EXCISION_REPAIR : chr [1:8] "POLB" "APEX1" "LIG1" "ADPRS" ...
#> $ REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY : chr [1:25] "RFC1" "RFC2" "POLD1" "POLB" ...
#> $ REACTOME_ACTIVATION_OF_BAD_AND_TRANSLOCATION_TO_MITOCHONDRIA : chr [1:15] "BAD" "BID" "AKT2" "YWHAE" ...
#> $ REACTOME_ACTIVATION_OF_NOXA_AND_TRANSLOCATION_TO_MITOCHONDRIA : chr [1:5] "E2F1" "TFDP2" "TP53" "PMAIP1" ...
#> $ REACTOME_BH3_ONLY_PROTEINS_ASSOCIATE_WITH_AND_INACTIVATE_ANTI_APOPTOTIC_BCL_2_MEMBERS : chr [1:9] "BAD" "BID" "BMF" "BBC3" ...
#> $ REACTOME_RELEASE_OF_APOPTOTIC_FACTORS_FROM_THE_MITOCHONDRIA : chr [1:7] "BAK1" "BAX" "GSDMD" "GSDME" ...
#> $ REACTOME_FORMATION_OF_APOPTOSOME : chr [1:11] "MAPK1" "XIAP" "MAPK3" "CARD8" ...
#> $ REACTOME_ACTIVATION_OF_CASPASES_THROUGH_APOPTOSOME_MEDIATED_CLEAVAGE : chr [1:6] "XIAP" "APAF1" "CASP9" "CASP3" ...
#> $ REACTOME_CYTOCHROME_C_MEDIATED_APOPTOTIC_RESPONSE : chr [1:13] "MAPK1" "XIAP" "MAPK3" "CARD8" ...
#> $ REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS : chr [1:38] "VIM" "CDH1" "DSG2" "CASP8" ...
#> $ REACTOME_SMAC_XIAP_REGULATED_APOPTOTIC_RESPONSE : chr [1:8] "XIAP" "SEPTIN4" "APAF1" "CASP9" ...
#> $ REACTOME_APOPTOTIC_FACTOR_MEDIATED_RESPONSE : chr [1:20] "BAK1" "BAX" "MAPK1" "XIAP" ...
#> $ REACTOME_OPIOID_SIGNALLING : chr [1:90] "CAMKK1" "PRKAR2B" "CAMK2B" "GNA15" ...
#> $ REACTOME_PKA_MEDIATED_PHOSPHORYLATION_OF_CREB : chr [1:20] "PRKAR2B" "PRKACA" "ADCY2" "PRKAR1A" ...
#> $ REACTOME_CAMK_IV_MEDIATED_PHOSPHORYLATION_OF_CREB : chr [1:10] "CAMKK1" "CAMK2B" "CAMK2A" "CAMKK2" ...
#> $ REACTOME_CA_DEPENDENT_EVENTS : chr [1:37] "CAMKK1" "PRKAR2B" "CAMK2B" "CAMK2A" ...
#> $ REACTOME_G_PROTEIN_MEDIATED_EVENTS : chr [1:54] "CAMKK1" "PRKAR2B" "CAMK2B" "GNA15" ...
#> $ REACTOME_ELECTRIC_TRANSMISSION_ACROSS_GAP_JUNCTIONS : chr [1:5] "PANX2" "PANX1" "GJA10" "GJD2" ...
#> $ REACTOME_PRESYNAPTIC_DEPOLARIZATION_AND_CALCIUM_CHANNEL_OPENING : chr [1:11] "CACNA2D2" "CACNB1" "CACNG4" "CACNA1A" ...
#> $ REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE : chr [1:51] "TSPOAP1" "SYN1" "SLC6A13" "SYT1" ...
#> $ REACTOME_NEUROTRANSMITTER_CLEARANCE : chr [1:11] "ACHE" "COMT" "SLC6A4" "ALDH2" ...
#> $ REACTOME_NEUROTRANSMITTER_RECEPTORS_AND_POSTSYNAPTIC_SIGNAL_TRANSMISSION : chr [1:205] "CAMKK1" "PRKAR2B" "CACNG3" "AP2B1" ...
#> $ REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES : chr [1:270] "CAMKK1" "PRKAR2B" "TSPOAP1" "CACNG3" ...
#> $ REACTOME_NEURONAL_SYSTEM : chr [1:411] "CAMKK1" "PRKAR2B" "TSPOAP1" "ABCC8" ...
#> $ REACTOME_FORMATION_OF_RNA_POL_II_ELONGATION_COMPLEX : chr [1:61] "POLR2J" "PAF1" "ELOA" "MNAT1" ...
#> $ REACTOME_IRS_MEDIATED_SIGNALLING : chr [1:48] "GAB2" "PIK3CB" "FGFR2" "FGFR3" ...
#> $ REACTOME_RAF_INDEPENDENT_MAPK1_3_ACTIVATION : chr [1:23] "JAK2" "MAPK1" "MAPK3" "TYK2" ...
#> $ REACTOME_MAPK1_ERK2_ACTIVATION : chr [1:9] "JAK2" "MAPK1" "TYK2" "MAP2K2" ...
#> $ REACTOME_SOS_MEDIATED_SIGNALLING : chr [1:7] "SOS1" "KRAS" "IRS1" "HRAS" ...
#> $ REACTOME_FORMATION_OF_THE_EARLY_ELONGATION_COMPLEX : chr [1:33] "POLR2J" "MNAT1" "POLR2B" "CTDP1" ...
#> $ REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2F1 : chr [1:13] "POLA2" "E2F1" "POLA1" "PPP2CB" ...
#> $ REACTOME_E2F_ENABLED_INHIBITION_OF_PRE_REPLICATION_COMPLEX_FORMATION : chr [1:9] "ORC1" "ORC6" "ORC2" "ORC4" ...
#> $ REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION : chr [1:22] "POLA2" "ORC1" "ORC6" "E2F1" ...
#> $ REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS : chr [1:30] "BAD" "BID" "TP63" "TP73" ...
#> $ REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS : chr [1:27] "PRKCH" "DGKG" "DGKA" "PRKCQ" ...
#> $ REACTOME_DISINHIBITION_OF_SNARE_FORMATION : chr [1:5] "STX4" "STXBP3" "PRKCG" "PRKCA" ...
#> $ REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE : chr [1:35] "FYN" "LCP2" "PIK3CB" "RHOA" ...
#> $ REACTOME_DOWNSTREAM_SIGNALING_EVENTS_OF_B_CELL_RECEPTOR_BCR : chr [1:81] "PSMB1" "PSMC4" "PSMA4" "CUL1" ...
#> $ REACTOME_ACTIVATION_OF_RAS_IN_B_CELLS : chr [1:5] "KRAS" "RASGRP3" "RASGRP1" "HRAS" ...
#> $ REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES : chr [1:82] "NUP160" "TPR" "EIF2AK2" "NDC1" ...
#> $ REACTOME_PROLACTIN_RECEPTOR_SIGNALING : chr [1:15] "CUL1" "JAK2" "RBX1" "GHR" ...
#> $ REACTOME_SIGNALING_BY_NODAL : chr [1:23] "MAPK1" "MAPK3" "ACVR2B" "FOXO3" ...
#> $ REACTOME_FERTILIZATION : chr [1:26] "CD9" "OVGP1" "B4GALT1" "CATSPERG" ...
#> $ REACTOME_MEIOTIC_SYNAPSIS : chr [1:77] "BRCA1" "SYNE2" "STAG3" "SMC1A" ...
#> $ REACTOME_ROS_AND_RNS_PRODUCTION_IN_PHAGOCYTES : chr [1:36] "MPO" "NOS2" "SLC11A1" "ATP6V0A1" ...
#> $ REACTOME_SIGNALING_BY_FGFR_IN_DISEASE : chr [1:63] "POLR2J" "GAB2" "POLR2B" "FGFR2" ...
#> $ REACTOME_SIGNALING_BY_ERBB2 : chr [1:50] "MATK" "FYN" "ERBB3" "RHOA" ...
#> $ REACTOME_SIGNALING_BY_ERBB2_IN_CANCER : chr [1:26] "ERBB3" "HSP90AA1" "CDC37" "GAB1" ...
#> $ REACTOME_REGULATION_OF_GENE_EXPRESSION_BY_HYPOXIA_INDUCIBLE_FACTOR : chr [1:11] "CREBBP" "EP300" "HIF1A" "CA9" ...
#> $ REACTOME_CELLULAR_RESPONSE_TO_HYPOXIA : chr [1:75] "CREBBP" "PSMB1" "PSMC4" "PSMA4" ...
#> $ REACTOME_CONSTITUTIVE_SIGNALING_BY_LIGAND_RESPONSIVE_EGFR_CANCER_VARIANTS : chr [1:19] "HSP90AA1" "CDC37" "GAB1" "CBL" ...
#> $ REACTOME_SIGNALING_BY_ERBB4 : chr [1:58] "GABRA1" "TAB2" "ERBB3" "NEDD4" ...
#> $ REACTOME_CROSS_PRESENTATION_OF_PARTICULATE_EXOGENOUS_ANTIGENS_PHAGOSOMES : chr [1:8] "CYBA" "ITGB5" "NCF4" "NCF2" ...
#> $ REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION : chr [1:106] "PSMB1" "BTK" "MRC2" "PSMC4" ...
#> $ REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY : chr [1:11] "LNPEP" "CTSL" "CTSV" "HLA-F" ...
#> $ REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES : chr [1:50] "PSMB1" "MRC2" "PSMC4" "PSMA4" ...
#> $ REACTOME_ERYTHROCYTES_TAKE_UP_CARBON_DIOXIDE_AND_RELEASE_OXYGEN : chr [1:13] "SLC4A1" "CYB5R4" "CA2" "RHAG" ...
#> $ REACTOME_METHIONINE_SALVAGE_PATHWAY : chr [1:6] "MRI1" "MTAP" "GOT1" "ENOPH1" ...
#> $ REACTOME_ERYTHROCYTES_TAKE_UP_OXYGEN_AND_RELEASE_CARBON_DIOXIDE : chr [1:9] "SLC4A1" "CA2" "RHAG" "CA1" ...
#> $ REACTOME_SHC1_EVENTS_IN_ERBB2_SIGNALING : chr [1:22] "ERBB3" "HBEGF" "SOS1" "EREG" ...
#> $ REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING : chr [1:10] "HBEGF" "PIK3CA" "EREG" "PIK3R1" ...
#> $ REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING : chr [1:14] "HBEGF" "SOS1" "EREG" "KRAS" ...
#> $ REACTOME_NUCLEAR_SIGNALING_BY_ERBB4 : chr [1:32] "TAB2" "PSEN1" "PGR" "ESR1" ...
#> $ REACTOME_DOWNREGULATION_OF_ERBB4_SIGNALING : chr [1:9] "NEDD4" "ITCH" "WWP1" "RPS27A" ...
#> $ REACTOME_INTERLEUKIN_7_SIGNALING : chr [1:36] "HGF" "IL7" "JAK3" "PIK3R2" ...
#> $ REACTOME_DEVELOPMENTAL_BIOLOGY : chr [1:1142] "CYP51A1" "PLXND1" "POLR2J" "CREBBP" ...
#> $ REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT : chr [1:65] "SLC25A13" "OTC" "CS" "IDH3G" ...
#> $ REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM : chr [1:719] "CRLF1" "MAP3K14" "TNFRSF12A" "RALA" ...
#> $ REACTOME_ADAPTIVE_IMMUNE_SYSTEM : chr [1:825] "CD99" "KLHL13" "CDC27" "FBXL3" ...
#> $ REACTOME_SPRY_REGULATION_OF_FGF_SIGNALING : chr [1:16] "MKNK1" "MAPK1" "MAPK3" "PPP2CB" ...
#> $ REACTOME_CA2_ACTIVATED_K_CHANNELS : chr [1:9] "KCNN2" "KCNN4" "KCNN1" "KCNMB4" ...
#> $ REACTOME_INWARDLY_RECTIFYING_K_CHANNELS : chr [1:35] "ABCC8" "ABCC9" "GNB5" "GNB1" ...
#> $ REACTOME_POTASSIUM_CHANNELS : chr [1:103] "ABCC8" "KCNG1" "KCNQ1" "KCNH2" ...
#> $ REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS : chr [1:43] "KCNG1" "KCNQ1" "KCNH2" "KCNAB2" ...
#> $ REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS : chr [1:12] "KCNK2" "KCNK16" "KCNK6" "KCNK10" ...
#> $ REACTOME_SPERM_MOTILITY_AND_TAXES : chr [1:9] "CATSPERG" "HVCN1" "CATSPERB" "CATSPER3" ...
#> $ REACTOME_ACROSOME_REACTION_AND_SPERM_OOCYTE_MEMBRANE_BINDING : chr [1:6] "CD9" "IZUMO4" "ACR" "IZUMO2" ...
#> $ REACTOME_GRB7_EVENTS_IN_ERBB2_SIGNALING : chr [1:5] "ERBB3" "ERBB2" "GRB7" "NRG1" ...
#> $ REACTOME_DOWNREGULATION_OF_ERBB2_ERBB3_SIGNALING : chr [1:13] "ERBB3" "AKT2" "AKT3" "USP8" ...
#> $ REACTOME_TRANSCRIPTION_OF_E2F_TARGETS_UNDER_NEGATIVE_CONTROL_BY_DREAM_COMPLEX : chr [1:19] "RBL1" "CDC6" "E2F1" "RBL2" ...
#> $ REACTOME_TRANSCRIPTION_OF_E2F_TARGETS_UNDER_NEGATIVE_CONTROL_BY_P107_RBL1_AND_P130_RBL2_IN_COMPLEX_WITH_HDAC1 : chr [1:16] "RBL1" "MYBL2" "E2F1" "RBL2" ...
#> $ REACTOME_MITOCHONDRIAL_IRON_SULFUR_CLUSTER_BIOGENESIS : chr [1:13] "HSCB" "ISCA1" "ISCU" "FDX1" ...
#> $ REACTOME_RORA_ACTIVATES_GENE_EXPRESSION : chr [1:18] "CREBBP" "RORA" "SREBF1" "SMARCD3" ...
#> $ REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_GENE_EXPRESSION : chr [1:27] "CREBBP" "ARNTL2" "F7" "SMARCD3" ...
#> $ REACTOME_ABC_TRANSPORTERS_IN_LIPID_HOMEOSTASIS : chr [1:18] "PEX3" "ABCA7" "ABCD1" "ABCA2" ...
#> $ REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS : chr [1:16] "TRPC7" "P2RX5" "P2RX7" "ITPR3" ...
#> $ REACTOME_ACTIVATION_OF_PUMA_AND_TRANSLOCATION_TO_MITOCHONDRIA : chr [1:9] "TP63" "TP73" "PPP1R13B" "E2F1" ...
#> $ REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION : chr [1:13] "KPNB1" "KPNA1" "H1-3" "H1-1" ...
#> $ REACTOME_CASPASE_ACTIVATION_VIA_DEATH_RECEPTORS_IN_THE_PRESENCE_OF_LIGAND : chr [1:16] "CFLAR" "FAS" "CASP8" "TRADD" ...
#> [list output truncated]