9 Pathogenesis Based Transcripts (PBT) gene sets specifically related to kidney transplant
Usage
data(PBT_gmt)Format
a gmt object containing 9 gene sets specific to kidney
transplant (see GSA.read.gmt), which is simply a
list with the 3 following components:
genesets: alistofngene identifiers vectors composing eachgene set (each gene set is represented as the vector of the gene identifiers composing it)geneset.names: a vector of lengthncontaining the gene set names (i.e. gene sets identifiers)geneset.descriptions: a vector of length
ncontaining gene set descriptions (e.g. textual information on their biological function)
References
Halloran PF, De Freitas DG, Einecke G, et al., The molecular phenotype of kidney transplants: Personal viewpoint, Am J Transplant, 10: 2215-2222, 2010. .
Sellares J, Reeve J, Loupy A, et al., Molecular diagnosis of antibody-mediated rejection in human kidney transplants, Am J Transplant, 13:971-983, 2013.
Broin PO, Hayde N, Bao Y, et al., A pathogenesis-based transcript signature in donor-specific antibody-positive kidney transplant patients with normal biopsies, Genomics Data 2: 357-60, 2014.
Examples
data('PBT_gmt')
PBT_gmt
#> $genesets
#> $genesets[[1]]
#> [1] "ABCB4" "ADAM28" "ALS2CR13" "AREG" "ARHGAP24" "BACE2"
#> [7] "BANK1" "BCL11A" "BCL2L11" "BCNP1" "BIRC3" "BLK"
#> [13] "BTLA" "BTNL9" "C13orf18" "C14orf110" "C3orf6" "C9orf45"
#> [19] "CCR6" "CD19" "CD1C" "CD22" "CD72" "CD79A"
#> [25] "CD79B" "CHPT1" "COCH" "CPNE5" "CR2" "DD5"
#> [31] "E2F5" "EAF2" "EBF" "ESRRBL1" "FCER2" "FCRH1"
#> [37] "FLJ12363" "FLJ13984" "FLJ20202" "FLJ32028" "FREB" "GABBR1"
#> [43] "GNG7" "GPR18" "HDAC9" "HERPUD1" "HLA-DOA" "HLA-DOB"
#> [49] "HTPAP" "IGKC" "IL28RA" "IRTA2" "ITPR1" "KIAA0125"
#> [55] "KIAA0746" "KIAA0819" "KLHL14" "LAF4" "LCN6" "LOC283663"
#> [61] "LOC284749" "LY9" "MEF2C" "MGC24039" "MGC40368" "MGC48332"
#> [67] "MOX2" "MS4A1" "NAP1L" "NR4A2" "OSBPL10" "P2RX5"
#> [73] "PAWR" "PAX5" "PCDH9" "PDLIM1" "PEG10" "PKIG"
#> [79] "PLEKHG1" "PNOC" "POU2AF1" "PRICKLE1" "RALGPS2" "RAM2"
#> [85] "RNF141" "SCN3A" "SEMA4B" "SLC15A2" "SNARK" "SPAP1"
#> [91] "SPIB" "STRBP" "TCF4" "TCF8" "TCL1A" "TLR10"
#> [97] "TM4SF13" "VPREB3" "ZDHHC23" "ZNF238"
#>
#> $genesets[[2]]
#> [1] "CDH13" "CDH5" "COL13A1" "CX3CR1" "DARC" "FGFBP2"
#> [7] "GNG11" "GNLY" "HLA-DRB3" "ICAM2" "KLRF1" "MALL"
#> [13] "MYBL1" "PGM5" "PLA1A" "PLAT" "ROBO4" "SH2D1B"
#> [19] "SOX7" "TEK" "TM4SF18"
#>
#> $genesets[[3]]
#> [1] "ACE" "ADCY4" "ADRA2A" "ALPL" "ANGPT1" "ANGPT2"
#> [7] "BMP6" "BMX" "CARD4" "CASP1" "CAV1" "CD34"
#> [13] "CD36" "CDH26" "CDH5" "CETP" "CMAH" "CSAH"
#> [19] "COL18A1" "COL4A1" "COL4A2" "CRIM1" "CTGF" "CYYR1"
#> [25] "DAB2" "DLC1" "DNAJB1" "EDG1" "EDN1" "EDN1"
#> [31] "ET1" "EFEMP1" "EHD4" "EMCN" "ENPEP" "ENPP2"
#> [37] "ESM1" "EVA1" "FABP4" "FGD5" "FHOD1" "FLI1"
#> [43] "FOSB" "FOXF2" "GEM" "GJA4" "GMFG" "HEYL"
#> [49] "HHIP" "HOXD1" "HOXD4" "HSPA6" "HSPG2" "HSU24186"
#> [55] "ICAM2" "IGFBP7" "JUNB" "KDR" "KLF4" "KMO"
#> [61] "LAMB1" "LAMC1" "LDB2" "LOXL2" "MAOB" "MCAM"
#> [67] "MEOX1" "MFNG" "MGP" "MLL3" "MSL3L1" "NFATC4"
#> [73] "NID2" "NOS3" "NOX4" "NP" "NPR1" "NR4A1"
#> [79] "NRF1" "NTN4" "NXF1" "OPN3" "PAK2" "PALMD"
#> [85] "PDGFB" "PDGFRB" "PECAM1" "PLSCR4" "PLVAP" "PODXL"
#> [91] "PPP1R16B" "PPP1R16B" "TIMAP" "ANKRD4" "KIAA0823" "PRG1"
#> [97] "PRKACA" "PTGIR" "RAI14" "RAMP2" "RASGRP2" "RASIP1"
#> [103] "RGS5" "RHOJ" "RPGR" "SDPR" "SEC14L1" "SELE"
#> [109] "SELP" "SERPINE1" "SNAI1" "SOX18" "TARSH" "TBX2"
#> [115] "TCF4" "TDO2" "TEK" "THBS1" "TRPV2" "TXNDC5"
#> [121] "UACA" "VCAM1" "VWF" "ZNF521"
#>
#> $genesets[[4]]
#> [1] "CPA3" "FCER1A" "TPSAB1" "TPSB2"
#>
#> $genesets[[5]]
#> [1] "SEPT4" "ACSL5" "AKAP2"
#> [4] "PALM2-AKAP2" "ANGPTL2" "ANKRD22"
#> [7] "APOBEC3F" "APOBEC3G" "APOBEC3G"
#> [10] "APOL1" "APOL2" "APOL3"
#> [13] "APOL4" "APOL6" "AQP1"
#> [16] "ARNT2" "ASPHD2" "ATF3"
#> [19] "BATF2" "BST2" "BTN3A1"
#> [22] "BTN3A2" "BTN3A2" "BTN3A3"
#> [25] "BTN3A3" "C19orf66" "C1orf21"
#> [28] "C1QB" "C1QC" "C1R"
#> [31] "C1S" "C2" "C4A"
#> [34] "C4B" "C4B_2" "C4orf32"
#> [37] "C5orf56" "C8orf4" "CARD16"
#> [40] "CASP1" "CASP1" "CCL2"
#> [43] "CCL20" "CCL8" "CCRL1"
#> [46] "CD274" "CD38" "CD40"
#> [49] "CD74" "CEBPD" "CFH"
#> [52] "CFHR1" "CLIC2" "CMPK2"
#> [55] "COL8A1" "CTSS" "CXCL10"
#> [58] "CXCL11" "CXCL2" "CXCL9"
#> [61] "DDIT4L" "DDX58" "DDX60"
#> [64] "DTX3L" "EDNRA" "EFCAB2"
#> [67] "EPSTI1" "F3" "FAM107A"
#> [70] "LOC101059937" "FAM117B" "FAM26F"
#> [73] "FBXO6" "FCGR1A" "FCGR1B"
#> [76] "FCGR1C" "FCGR1B" "GABBR1"
#> [79] "UBD" "GBP1" "GBP2"
#> [82] "GBP3" "GBP4" "GBP5"
#> [85] "GCH1" "GZMA" "HCAR3"
#> [88] "HCP5" "HLA-A" "HLA-B"
#> [91] "HLA-C" "HLA-DMA" "HLA-DMB"
#> [94] "HLA-DOA" "HLA-DPA1" "HLA-DPB1"
#> [97] "HLA-DQA1" "HLA-DQA2" "LOC100509457"
#> [100] "HLA-DQA1" "LOC100509457" "HLA-DQB1"
#> [103] "HLA-DQB1" "LOC101060835" "HLA-DRA"
#> [106] "HLA-DRB1" "HLA-DRB3" "HLA-DRB4"
#> [109] "LOC100507709" "LOC100507714" "HLA-DRB1"
#> [112] "HLA-DRB4" "HLA-DRB5" "LOC100507709"
#> [115] "LOC100507714" "HLA-DRB1" "HLA-DRB4"
#> [118] "LOC100507709" "LOC100507714" "HLA-DRB1"
#> [121] "LOC100507709" "LOC100507714" "HLA-DRB4"
#> [124] "HLA-E" "HLA-F" "HLA-G"
#> [127] "HLA-J" "ICAM1" "IDO1"
#> [130] "IDO2" "IFI27" "IFI30"
#> [133] "PIK3R2" "IFI35" "IFI44"
#> [136] "IFI44L" "IFI6" "IFIH1"
#> [139] "IFIT1" "IFIT2" "IFIT3"
#> [142] "IFIT5" "IFITM1" "IFITM1"
#> [145] "IFITM2" "IL15" "IL15RA"
#> [148] "IL18BP" "IL32" "IRF1"
#> [151] "IRF8" "IRF9" "ISG15"
#> [154] "ISG20" "ITGA6" "JAK2"
#> [157] "KCNJ2" "KCTD14" "NDUFC2-KCTD14"
#> [160] "KLF4" "LAP3" "LGALS3BP"
#> [163] "LGALS9" "LIMK2" "LMNB1"
#> [166] "LOC100129518" "SOD2" "LOC154761"
#> [169] "LRRK2" "MAP3K7CL" "MDK"
#> [172] "MICB" "MIR5193" "UBA7"
#> [175] "MX1" "N4BP2L1" "NLRC5"
#> [178] "NME7" "NRK" "NTN4"
#> [181] "OAS1" "OAS2" "OAS3"
#> [184] "OTTHUMG00000159342" "RP1-93H18.6" "P2RY14"
#> [187] "PARP12" "PARP14" "PARP9"
#> [190] "PCDH7" "PCLO" "PDE4B"
#> [193] "PIGR" "PIK3AP1" "PLA1A"
#> [196] "PLSCR1" "PMAIP1" "PSMB10"
#> [199] "PSMB8" "PSMB9" "PSME2"
#> [202] "PSTPIP2" "RARRES1" "RARRES3"
#> [205] "RELN" "RHOBTB3" "RIPK2"
#> [208] "RND3" "RNF19B" "RNF213"
#> [211] "RTP4" "SAA1" "SAA2"
#> [214] "SAA2-SAA4" "SAMD9L" "SAMHD1"
#> [217] "SECTM1" "SERPING1" "SLAMF7"
#> [220] "SLC15A3" "SLC27A2" "SLC2A5"
#> [223] "SLC6A12" "SOCS1" "SOCS3"
#> [226] "SOD2" "SP110" "SP140L"
#> [229] "SRGN" "STAMBPL1" "STAT1"
#> [232] "STAT2" "SUCNR1" "TAGAP"
#> [235] "TAP1" "TAP2" "TAPBPL"
#> [238] "TGM2" "TIFA" "TNC"
#> [241] "TNFAIP2" "TNFAIP6" "TNFSF10"
#> [244] "TNFSF13B" "TNFSF15" "TOX3"
#> [247] "TRIM21" "TRIM22" "TRIM69"
#> [250] "TYMP" "UBE2L6" "USP6NL"
#> [253] "VAMP5" "VRK2" "WARS"
#> [256] "XAF1"
#>
#> $genesets[[6]]
#> [1] "CX3CR1" "KLRF1" "MYBL1" "SH2D1B"
#>
#> $genesets[[7]]
#> [1] "CD2" "CD3D" "CD8A" "CST7" "CXCR6" "GNLY"
#> [7] "GZMA" "GZMB" "GZMK" "H963" "HOP" "IFNG"
#> [13] "IL2RB" "ITK" "KIAA0101" "KLRK1" "LCK" "NELL2"
#> [19] "NKG7" "NUSAP1" "PRF1" "RRM2" "STAT4" "TRA@"
#> [25] "TRGV9"
#>
#> $genesets[[8]]
#> [1] "ADAMDEC1" "APOBEC3A" "C14orf58" "C1orf38" "CCL18" "CCRL2"
#> [7] "CD36" "CD68" "CD86" "CEBPA" "CENTA2" "CES1"
#> [13] "CSF1R" "CSF2RA" "CSTA" "CXCL16" "ECGF1" "EMILIN2"
#> [19] "FCER1G" "FCGR2A" "FLJ10116" "FLJ13213" "FLJ22570" "FPR1"
#> [25] "FPRL2" "GCA" "GJB2" "HID" "KID" "PPK"
#> [31] "CX26" "DFNA3" "DFNB1" "NSRD1" "GM2A" "GPR77"
#> [37] "HK3" "IBRDC3" "IFIT4" "IGSF6" "IL1RN" "IL4I1"
#> [43] "ILT8" "LILRB6" "IRF2" "KYNU" "LILRB2" "LILRB3"
#> [49] "LILRB4" "LYZ" "MCOLN1" "MICL" "MNDA" "MS4A7"
#> [55] "NCF2" "NKIR" "NMES1" "PDE4DIP" "PILRA" "PLA2G7"
#> [61] "PRKCD" "PTAFR" "PAFR" "RC3" "S100A9" "SIGLEC7"
#> [67] "SLAMF8" "SLC15A3" "SLC1A3" "SLC29A3" "SLC38A6" "SN"
#> [73] "TFEC" "TLR2" "TLR8" "UNC93B1"
#>
#> $genesets[[9]]
#> [1] "CD3D" "CXCR6" "GPR171" "NELL2" "TCRA"
#>
#>
#> $geneset.name
#> $geneset.name[[1]]
#> [1] "BAT"
#>
#> $geneset.name[[2]]
#> [1] "DSAST"
#>
#> $geneset.name[[3]]
#> [1] "ENDATs"
#>
#> $geneset.name[[4]]
#> [1] "MAT"
#>
#> $geneset.name[[5]]
#> [1] "nGRIT"
#>
#> $geneset.name[[6]]
#> [1] "NKB"
#>
#> $geneset.name[[7]]
#> [1] "QCAT"
#>
#> $geneset.name[[8]]
#> [1] "QCMAT"
#>
#> $geneset.name[[9]]
#> [1] "TCB"
#>
#>
#> $geneset.description
#> $geneset.description[[1]]
#> [1] "B-cell associated transcripts"
#>
#> $geneset.description[[2]]
#> [1] "Donor-specific antibody (DSA) selective transcripts"
#>
#> $geneset.description[[3]]
#> [1] "Endothelial cell associated transcripts"
#>
#> $geneset.description[[4]]
#> [1] "Mast cell associated transcripts"
#>
#> $geneset.description[[5]]
#> [1] "New Gamma-IFN and Rejection Induced Transcripts"
#>
#> $geneset.description[[6]]
#> [1] "NK cell transcript burden"
#>
#> $geneset.description[[7]]
#> [1] "Quantitative CTL-Associated Transcripts"
#>
#> $geneset.description[[8]]
#> [1] "Quantitative Constitutive Macrophage-Associated Transcripts"
#>
#> $geneset.description[[9]]
#> [1] "T cell transcript burden"
#>
#>