c2.all.v7.2.symbols: msidb c2 genesets

In SaritaPoonia/unCTC: Characterising single circulating tumor cell transcriptomes

msidb c2 genesets

Description

cr MsiDB This collection contains gene sets selected from multiple sources, including online pathway databases and biomedical literature. Many sets are also contributed by specific domain specialists.

Usage

data("c2.all.v7.2.symbols")

Format

The format is: List of 6229 $ BIOCARTA_FEEDER_PATHWAY : chr [1:9] "MPI" "HK1" "KHK" "PGM1" ... $ BIOCARTA_PROTEASOME_PATHWAY : chr [1:19] "RPN1" "PSMA1" "PSMA5" "RPN2" ... $ BIOCARTA_KREB_PATHWAY : chr [1:8] "FH" "SDHA" "OGDH" "SUCLA2" ... $ ST_INTERFERON_GAMMA_PATHWAY : chr [1:10] "STAT1" "PLA2G2A" "IFNG" "JAK2" ... $ ST_WNT_CA2_CYCLIC_GMP_PATHWAY : chr [1:20] "ITPR1" "PDE6H" "CAMK2D" "PDE6D" ... $ ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS : chr [1:47] "EGR3" "PTPN11" "NTRK1" "TUBA1A" ... $ ST_TUMOR_NECROSIS_FACTOR_PATHWAY : chr [1:29] "NFKBIA" "MAP3K7" "TNFRSF1A" "MAP3K3" ... $ ST_ERK1_ERK2_MAPK_PATHWAY : chr [1:32] "SOS1" "RPS6KA3" "TRAF3" "CREB3" ... $ ST_GA12_PATHWAY : chr [1:23] "PLD1" "RAF1" "EPHB2" "VAV1" ... $ ST_G_ALPHA_S_PATHWAY : chr [1:16] "RAF1" "RAPGEF3" "CAMP" "BRAF" ... $ ST_G_ALPHA_I_PATHWAY : chr [1:36] "RAP1GAP" "EGFR" "PLCB2" "SOS1" ... $ ST_IL_13_PATHWAY : chr [1:7] "IL13" "IL13RA2" "JAK2" "IL13RA1" ... $ ST_P38_MAPK_PATHWAY : chr [1:37] "MAP3K10" "MAP3K7" "MAPK14" "CREB3" ... $ ST_JAK_STAT_PATHWAY : chr [1:9] "PIAS1" "JAK3" "JAK2" "CISH" ... $ ST_GRANULE_CELL_SURVIVAL_PATHWAY : chr [1:28] "CXCR2" "CREB3" "ADCYAP1" "MAPK8IP2" ... $ ST_ADRENERGIC : chr [1:37] "GNA15" "EGFR" "MAPK14" "AKT1" ... $ ST_INTEGRIN_SIGNALING_PATHWAY : chr [1:82] "ANGPTL2" "PAK3" "ARHGAP35" "ITGA4" ... $ ST_GAQ_PATHWAY : chr [1:28] "NFKBIA" "AKT1" "VN1R1" "NFKBIB" ... $ ST_GA13_PATHWAY : chr [1:37] "RDX" "NFKBIA" "AKT1" "TBXA2R" ... $ ST_STAT3_PATHWAY : chr [1:11] "JAK3" "JAK2" "CISH" "SRC" ... $ ST_T_CELL_SIGNAL_TRANSDUCTION : chr [1:45] "PAK4" "LAT" "ZAP70" "VAV1" ... $ ST_TYPE_I_INTERFERON_PATHWAY : chr [1:9] "STAT1" "IRF9" "STAT2" "REG1A" ... $ ST_PAC1_RECEPTOR_PATHWAY : chr [1:8] "GNAQ" "ITPKA" "CAMP" "ADCYAP1" ... $ ST_B_CELL_ANTIGEN_RECEPTOR : chr [1:40] "CD19" "PPP1R13B" "VAV1" "NFKBIA" ... $ ST_INTERLEUKIN_4_PATHWAY : chr [1:26] "PPP1R13B" "INPP5D" "JAK2" "SOS1" ... $ ST_WNT_BETA_CATENIN_PATHWAY : chr [1:34] "PSEN1" "CER1" "DKK4" "NKD1" ... $ ST_JNK_MAPK_PATHWAY : chr [1:40] "DUSP8" "MAP3K10" "PAPPA" "MAP3K7" ... $ ST_FAS_SIGNALING_PATHWAY : chr [1:66] "TUFM" "EZR" "SMPD1" "MET" ... $ ST_MYOCYTE_AD_PATHWAY : chr [1:28] "RAC1" "RHO" "AKT1" "ITPR2" ... $ ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY : chr [1:38] "A1BG" "YWHAZ" "PPP1R13B" "INPP5D" ... $ REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND : chr [1:11] "POLD1" "POLD3" "RPA3" "POLD2" ... $ BLANCO_MELO_SARS_COV_1_INFECTION_MCR5_CELLS_UP : chr [1:12] "CENPE" "ASPM" "ESM1" "KIF20B" ... $ BLANCO_MELO_SARS_COV_1_INFECTION_MCR5_CELLS_DN : chr [1:9] "RGCC" "FGFR4" "BMP4" "INHBB" ... $ BLANCO_MELO_MERS_COV_INFECTION_MCR5_CELLS_UP : chr [1:295] "HSPA6" "HSPA7" "HSPA1B" "HSPA1A" ... $ BLANCO_MELO_MERS_COV_INFECTION_MCR5_CELLS_DN : chr [1:37] "ATP5F1D" "DNAJC12" "PTGDS" "CHCHD2" ... $ BLANCO_MELO_INFLUENZA_A_INFECTION_A594_CELLS_UP : chr [1:41] "CCL5" "PYGM" "HSPA6" "LINC00641" ... $ BLANCO_MELO_INFLUENZA_A_INFECTION_A594_CELLS_DN : chr [1:118] "MAFG" "WDR18" "COL4A4" "BAX" ... $ BLANCO_MELO_HUMAN_PARAINFLUENZA_VIRUS_3_INFECTION_A594_CELLS_UP : chr [1:204] "IFIT2" "IFNL1" "OASL" "IFIT1" ... $ BLANCO_MELO_HUMAN_PARAINFLUENZA_VIRUS_3_INFECTION_A594_CELLS_DN : chr [1:122] "H1-10-AS1" "ADM5" "CHTF18" "TIGD3" ... $ BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_UP : chr [1:285] "OASL" "IFNL1" "IFIT2" "IFIT1" ... $ BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_DN : chr [1:119] "ITGA11" "CDCA7L" "MCF2L" "CCER2" ... $ BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_CELLS_UP : chr [1:86] "INHBE" "ADM2" "STC2" "IL1A" ... $ BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_CELLS_DN : chr [1:77] "HNF1A-AS1" "SPEF1" "SDF2L1" "RADIL" ... $ BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_CALU3_CELLS_UP : chr [1:338] "IFNB1" "IFNL2" "IFNL3" "IFNL1" ... $ BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_CALU3_CELLS_DN : chr [1:24] "MIR31HG" "TEX15" "H2AX" "SNRNP25" ... $ BLANCO_MELO_COVID19_SARS_COV_2_LOW_MOI_INFECTION_A594_ACE2_EXPRESSING_CELLS_UP : chr [1:174] "EGR1" "CCL20" "CXCL2" "CXCL8" ... $ BLANCO_MELO_COVID19_SARS_COV_2_LOW_MOI_INFECTION_A594_ACE2_EXPRESSING_CELLS_DN : chr [1:14] "CPM" "ALDH1L2" "DPP4" "KRT4" ... $ BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_UP : chr [1:542] "EGR1" "CMPK2" "IFNB1" "IFI44" ... $ BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_DN : chr [1:96] "SEMA3E" "FLRT2" "AKR1C4" "ANXA2" ... $ BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_RUXOLITINIB_UP : chr [1:483] "EGR1" "BHLHE41" "NR1D1" "PPP4R4" ... $ BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_RUXOLITINIB_DN : chr [1:76] "GPX2" "ALDH1A1" "ASB9" "ETFB" ... $ BLANCO_MELO_COVID19_BRONCHIAL_EPITHELIAL_CELLS_SARS_COV_2_INFECTION_UP : chr [1:144] "CSF3" "CCL20" "CXCL5" "SPRR2D" ... $ BLANCO_MELO_COVID19_BRONCHIAL_EPITHELIAL_CELLS_SARS_COV_2_INFECTION_DN : chr [1:58] "PDE5A" "SPTLC3" "ALDH3A1" "MN1" ... $ BLANCO_MELO_BETA_INTERFERON_TREATED_BRONCHIAL_EPITHELIAL_CELLS_UP : chr [1:378] "IFIT3" "IFIT1" "IFIT2" "MX1" ... $ BLANCO_MELO_BETA_INTERFERON_TREATED_BRONCHIAL_EPITHELIAL_CELLS_DN : chr [1:216] "CSTA" "MZF1" "IFITM10" "CCDC88B" ... $ BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_INFECTION_UP : chr [1:136] "ITGA7" "HERC5" "PYGM" "XAF1" ... $ BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_INFECTION_DN : chr [1:81] "ANKRD23" "MND1" "RECQL4" "CCDC34" ... $ BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_DEL_NS1_INFECTION_UP : chr [1:644] "IFIT2" "IFIT1" "RSAD2" "CXCL10" ... $ BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_DEL_NS1_INFECTION_DN : chr [1:187] "RHNO1" "RAD51" "CDCA7" "CES3" ... $ BLANCO_MELO_COVID19_SARS_COV_2_POS_PATIENT_LUNG_TISSUE_UP : chr [1:172] "FDCSP" "RNASE2" "SELL" "CYP19A1" ... $ BLANCO_MELO_COVID19_SARS_COV_2_POS_PATIENT_LUNG_TISSUE_DN : chr [1:175] "SFN" "DPH7" "THAP2" "SPSB3" ... $ BUFFA_HYPOXIA_METAGENE : chr [1:50] "VEGFA" "SLC2A1" "PGAM1" "ENO1" ... $ NAKAMURA_CANCER_MICROENVIRONMENT_UP : chr [1:28] "HBA1" "PRSS2" "COL1A2" "GPIHBP1" ... $ NAKAMURA_CANCER_MICROENVIRONMENT_DN : chr [1:46] "CDC20" "RFC4" "RFC5" "CTH" ... $ WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP : chr [1:22] "DTL" "PCSK6" "PRC1" "KIF20A" ... $ WEST_ADRENOCORTICAL_TUMOR_MARKERS_DN : chr [1:20] "MFAP5" "IGFBP5" "KCNQ1" "RARRES2" ... $ WINTER_HYPOXIA_UP : chr [1:95] "HAUS2" "PTGFRN" "PYGL" "SLC6A8" ... $ WINTER_HYPOXIA_DN : chr [1:52] "CD48" "ANKRD44" "SYNRG" "GIMAP1" ... $ PARENT_MTOR_SIGNALING_UP : chr [1:568] "MSRB1" "IL17RC" "CTH" "VAT1" ... $ PARENT_MTOR_SIGNALING_DN : chr [1:44] "ELOVL5" "MAGEA9" "ITGAM" "KRT86" ... $ PYEON_HPV_POSITIVE_TUMORS_UP : chr [1:99] "PER3" "USP1" "SMARCA2" "ABCA17P" ... $ PYEON_HPV_POSITIVE_TUMORS_DN : chr [1:10] "NAP1L2" "PTHLH" "KLK8" "KLK10" ... $ NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP : chr [1:284] "MRPL42" "PNP" "NUDT5" "ETS1" ... $ NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN : chr [1:644] "TTC3" "SNHG7" "RAB40C" "B4GALT5" ... $ PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP : chr [1:211] "EMILIN1" "KCNMA1" "CSRP2" "RPE" ... $ PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN : chr [1:137] "MYLIP" "CBX4" "NR4A2" "CREM" ... $ LU_TUMOR_VASCULATURE_UP : chr [1:29] "WDR77" "TNFAIP6" "FJX1" "ISG15" ... $ LU_TUMOR_VASCULATURE_DN : chr [1:13] "ARX" "ABI3BP" "CELF2" "PRKAR2B" ... $ KORKOLA_EMBRYONAL_CARCINOMA_UP : chr [1:42] "LRP6" "NANOG" "C12orf57" "PLBD1" ... $ KORKOLA_EMBRYONAL_CARCINOMA_DN : chr [1:13] "SOX5" "LINC02366" "LRRC23" "H2AJ" ... $ KORKOLA_TERATOMA_UP : chr [1:17] "C12orf57" "CCND2" "ITFG2" "RECQL" ... $ KORKOLA_YOLK_SAC_TUMOR_UP : chr [1:20] "GAPDH" "DDX47" "TPI1" "SLC2A3" ... $ KORKOLA_CHORIOCARCINOMA_UP : chr [1:6] "CD9" "TPI1" "PLBD1" "GAPDH" ... $ KORKOLA_CHORIOCARCINOMA_DN : chr [1:11] "CLEC12B" "ACRBP" "CASC1" "RASSF8" ... $ KORKOLA_SEMINOMA_UP : chr [1:44] "TEAD4" "CD27" "DSTNP2" "ARHGDIB" ... $ KORKOLA_SEMINOMA_DN : chr [1:13] "LRRC23" "CLEC12B" "SOX5" "RASSF8" ... $ WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP : chr [1:113] "BTN3A1" "NELFA" "GAS6" "TRIM44" ... $ WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN : chr [1:93] "MAP4" "SCARB1" "WSB1" "SPR" ... $ HOLLMANN_APOPTOSIS_VIA_CD40_UP : chr [1:203] "ATP8A1" "PPP3CC" "TUBA1A" "MAP4K4" ... $ HOLLMANN_APOPTOSIS_VIA_CD40_DN : chr [1:267] "MSRB2" "CDKN1B" "HLA-DRB4" "VPS72" ... $ LIU_PROSTATE_CANCER_UP : chr [1:98] "BEND4" "CAMKK2" "TRIM68" "SOX4" ... $ LIU_PROSTATE_CANCER_DN : chr [1:491] "ITGA8" "ARHGEF40" "AKAP12" "VEGFA" ... $ LIU_SOX4_TARGETS_UP : chr [1:139] "ATP2B4" "INTS9" "TMSB10" "KLHL24" ... $ LIU_SOX4_TARGETS_DN : chr [1:310] "SHROOM3" "SURF6" "DECR1" "KIAA0319L" ... $ ONKEN_UVEAL_MELANOMA_UP : chr [1:790] "BAZ2B" "SNW1" "ADAM23" "CDC25B" ... $ ONKEN_UVEAL_MELANOMA_DN : chr [1:529] "SMARCC1" "CSNK2A2" "EIF2D" "RAB11FIP1" ... $ BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP : chr [1:206] "YBX3" "CALHM6" "CDCP1" "RILPL2" ... $ BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN : chr [1:180] "ZBTB43" "LSP1P4" "SNHG14" "ATL1" ... $ SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP : chr [1:352] "LPXN" "NUAK1" "IL1R1" "SPARC" ... [list output truncated]

Examples

data(c2.all.v7.2.symbols)
## maybe str(c2.all.v7.2.symbols) ; plot(c2.all.v7.2.symbols) ...

SaritaPoonia/unCTC documentation built on Nov. 8, 2022, 12:07 p.m.