duplicate gene id in TCGA GEX about curatedpcadata HOT 4 CLOSED

Also found the same issue with Taylor

taylor.gex <- curatedPCaData::mae_taylor[["gex"]]
dim(taylor.gex)
[1] 17638 300
row.names(taylor.gex)[duplicated(row.names(taylor.gex))]
[1] "ABCB9" "ABHD2" "ADAMTS6" "ADAMTSL1" "ADAMTSL4" "AFG3L1P" "AGAP6" "AGPAT3" "ALG13" "ANKRD36B" "ANKS6"
[12] "ARHGAP19" "ARHGAP27" "ARHGEF10" "ARID5A" "ATL3" "ATP11B" "ATP13A4" "ATP6V1C2" "ATXN7L1" "BACH1" "BIRC5"
[23] "BMP8A" "BOD1L1" "BRK1" "BTN3A2" "BZW1" "C1orf86" "C1QTNF5" "C21orf62" "C4orf3" "CACNA1C" "CCDC108"
[34] "CCDC127" "CCDC144A" "CCDC150" "CCDC57" "CCDC93" "CCNL2" "CD22" "CEP128" "CHRNA7" "CLIC5" "COX7A2"
[45] "CPLX2" "CRB2" "CSH1" "CYP2A7" "CYP2R1" "DBF4B" "DENND1B" "DGCR14" "DIDO1" "DIP2B" "DKK3"
[56] "DLG2" "DNAH10" "DNAH3" "DNAH6" "DNHD1" "DPY19L2P2" "EEF1D" "EPHA10" "EPHA6" "FAM13A" "FAM91A1"
[67] "FANCI" "FKBP9" "FOLH1" "FOXK2" "FSD1L" "FSIP2" "FZD5" "GFOD1" "GLIS3" "GNA11" "GNAI2"
[78] "GOLGA8B" "GPR107" "GPR110" "GPR26" "GRK5" "H2AFV" "HEATR1" "HIP1" "HIST1H2BJ" "HIST1H3I" "IGF1R"
[89] "IGF2" "INF2" "ING5" "KALRN" "KIAA0101" "KIAA0125" "KIAA1456" "KIF24" "KIF5A" "KIR2DL4" "KLHDC10"
[100] "LASP1" "LINC00982" "LMBR1" "LNPEP" "LPHN1" "LRRFIP1" "LRRIQ3" "LRRK1" "LSM14B" "LSM14B" "LYRM4"
[111] "LYRM7" "MAFK" "MB" "MBP" "MCM9" "MECOM" "MEGF8" "MMP16" "MYCN" "MZT2B" "N4BP2L1"
[122] "NAIF1" "NCKAP5" "NDUFS4" "NEK10" "NHLRC2" "NOL4L" "NPR3" "NUDT22" "ORAOV1" "P4HA2" "PANK2"
[133] "PCDH11X" "PCID2" "PCLO" "PGPEP1" "PHLDB2" "PHLDB3" "PIEZO2" "PLB1" "PLXNA2" "PPIH" "PRR13"
[144] "PRR14L" "PRRC2B" "PRRC2B" "PRUNE2" "PSD3" "PTEN" "PTGR1" "PXN" "RAB3IP" "RAPGEF1" "RASGRF1"
[155] "RBM14" "RBM6" "RBMS1" "REEP3" "RFT1" "RGSL1" "RNF17" "RNF207" "RNF213" "ROPN1B" "RPL14"
[166] "RPL23AP7" "RPL27A" "RSC1A1" "RUSC1-AS1" "SAA1" "SAP25" "SCN8A" "SEC62" "SERHL2" "SH3PXD2A" "SHISA6"
[177] "SHPK" "SLC1A5" "SLC25A37" "SLC7A14" "SMAD2" "SNRPN" "SORBS2" "SPAG11B" "SPEM1" "SPTB" "SRP19"
[188] "ST8SIA2" "STMN1" "STX1B" "SZT2" "TAMM41" "TBC1D16" "TEAD1" "TF" "TMEM51-AS1" "TOM1L1" "TOM1L2"
[199] "TOR1AIP2" "TRA2A" "TRERF1" "TRMT44" "TSHZ2" "TSPAN9" "TTC40" "TUBB2B" "UBE2D3" "UNKL" "VANGL1"
[210] "VKORC1L1" "VPS53" "WDFY4" "WDR90" "WNK1" "XKR6" "YIF1B" "ZC3HAV1L" "ZDHHC20" "ZDHHC3" "ZNF384"
[221] "ZNF385C" "ZNF479" "ZNF678" "ZNF706" "ZNF75A" "ZNF8" "ZRANB1" "ZXDC"
taylor.gex <- ExpressionSet(assayData=taylor.gex[!duplicated(row.names(taylor.gex)),])
dim(taylor.gex)
Features Samples
17410 300

from curatedpcadata.

I've managed to track down the source of this issue; it comes down into differences in how biomaRt and cBioPortal handle gene symbols and aliases. Looks like for example RCAN1 and CSP1 are both mapped into RCAN1 in cBioPortal, while querying these from Ensembl database with biomaRt it assigns them separate gene symbols. The other duplicated is RCAN2. Why Ensembl returns separate gene symbols is unknown to me, so I'll have to think if I can come up with a generalized solution or just work one out for RCAN1 & RCAN2 (and their potential aliases):

> head(cgdsr::getProfileData(mycgds, genes = c("RCAN1", "CSP1"), geneticProfile = "prad_tcga_pub_rna_seq_v2_mrna", caseList = "prad_tcga_pub_sequenced"))
                   RCAN1  RCAN1.1
TCGA.EJ.5502.01 660.5782 660.5782
TCGA.HC.7209.01 469.9961 469.9961
TCGA.HC.7748.01 349.4016 349.4016
TCGA.J4.A83N.01 390.1099 390.1099
TCGA.2A.A8VV.01 238.6163 238.6163
TCGA.2A.A8VT.01 325.7353 325.7353
> c("RCAN1", "CSP1") %in% unique(curatedPCaData:::curatedPCaData_genes$hgnc_symbol)
[1] TRUE TRUE

from curatedpcadata.

Interestingly, gene cards lists CSP1 as an alias for RCAN1 but not vice versa (querying for CSP1 yields unique gene not connected to RCAN1; one is located on chromosome 2 other in 21):

https://www.genecards.org/cgi-bin/carddisp.pl?gene=RCAN1
https://www.genecards.org/cgi-bin/carddisp.pl?gene=CSP1

from curatedpcadata.

These gene mappings are not no longer an issue as we don't query from cBio:

> table(duplicated(row.names(mae_tcga[["gex.fpkm"]])))

FALSE 
58387 
> table(duplicated(row.names(mae_taylor[["gex.rma"]])))

FALSE 
17410

from curatedpcadata.