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Annotation File Discrepancies

CountGene NameComposite Element REFCohort(s)
1EIF4EBP14E-BP1_pT37THCA
53EIF4EBP14E-BP1_pT37_T46ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
1EIF4EBP14E-BP1_pT37T46HNSC
47TUBA1BAcetyl-a-Tubulin-Lys40ACC,BLCA,BRCA,CESC,COAD,ESCA,GBM,KIRC,KIRP,LGG,LUAD,LUSC,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,THCA,UCEC,UCS,UVM
8TUBA1BAcetyl-a-Tubulin(Lys40)CHOL,DLBC,KICH,LGG,LIHC,MESO,TGCT,THYM
1NCOA3AIB1THCA
18CTNNA1alpha-CateninBLCA,BRCA,COAD,GBM,HNSC,KIRC,LGG,LUAD,LUSC,OV,PRAD,READ,SKCM,STAD,THCA,UCEC
21CTNNB1alpha-CateninACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
8ANXA1Annexin_1CHOL,DLBC,KICH,LGG,LIHC,MESO,TGCT,THYM
2ANXA1Annexin_IHNSC,THCA
33ANXA7Annexin_VIIBLCA,BRCA,COAD,GBM,KIRC,LGG,LUAD,LUSC,OV,PRAD,READ,SKCM,STAD,THCA,UCEC
21ANXA7 Annexin_VIIACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
45ANXA1Annexin-1ACC,BLCA,BRCA,CESC,COAD,ESCA,GBM,KIRC,KIRP,LGG,LUAD,LUSC,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,THCA,UCEC,UCS,UVM
21ARHIARHIACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
2BAP1ARHITHCA
28DIRAS3ARHIBLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,UCEC
50BAP1Bap1-c-4BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
2SQSTM1Bap1-c-4THCA
3BAP1Bap1c-4ACC,KIRP,PAAD
1BCL2L1Bcl-XTHCA
34CTNNB1beta-CateninBLCA,BRCA,COAD,GBM,HNSC,KIRC,LGG,LUAD,LUSC,OV,PRAD,READ,SKCM,STAD,THCA,UCEC
21CTNNB2beta-CateninACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
1CA9KIRC
1CASP3Caspase-3_activeTHCA
1CD20CD20THCA
54MS4A1CD20ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,HNSC,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
1CD49CD49bTHCA
54ITGA2CD49bACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,HNSC,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
25CDC2CDK1ACC,CESC,CHOL,DLBC,ESCA,HNSC,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
30CDK1CDK1BLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,THCA,UCEC
1Complex-II_subunit30KIRC
1PTGS2COX-2THCA
4DIRAS3Di-Ras3LGG,PRAD,STAD,THCA
1PTK2FAKTHCA
30GAB2GAB2BLCA,BRCA,COAD,GBM,HNSC,KIRC,LUAD,LUSC,OV,READ,SKCM,THCA,UCEC
25GAB2Gab2ACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THCA,THYM,UCS,UVM
1GYG-Glycogenin1KIRC
1GYSKIRC
1GYS_pS641KIRC
55ERBB3HER3_pY1289ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,HNSC,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
1ERBB3HER3_pY1298THCA
1HIF-1_alphaKIRC
1IGF1RIGF-1R-betaTHCA
5MAPK8JNK_pT183_pT185KICH,LGG,LIHC,MESO,THCA
50MAPK8JNK_pT183_pY185ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,HNSC,KIRC,KIRP,LGG,LUAD,LUSC,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
1LDHAKIRC
1LDHBKIRC
1MitochondriaKIRC
25FRAP1mTORACC,CESC,CHOL,DLBC,ESCA,HNSC,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
30MTORmTORBLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,THCA,UCEC
25FRAP1mTOR_pS2448ACC,CESC,CHOL,DLBC,ESCA,HNSC,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
30MTORmTOR_pS2448BLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,THCA,UCEC
43MYH9Myosin-IIa_pS1943BLCA,BRCA,CESC,COAD,ESCA,GBM,KIRC,KIRP,LGG,LUAD,LUSC,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,THCA,UCEC,UCS,UVM
8MYH9Myosin-Iia_pS1943CHOL,DLBC,KICH,LGG,LIHC,MESO,TGCT,THYM
3MYH9Myosin-IIa-pS1943ACC,KIRP,PAAD
1NEK7NEK7THCA
1NOTCH3Notch3THCA
1Oxphos-complex-V_subunitbKIRC
1P-REX1THCA
2PRDX1p62-LCK-ligandTHCA
53SQSTM1p62-LCK-ligandACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
54SERPINE1PAI-1ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,HNSC,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
1PAI-1Pal-1THCA
1PEA-15PEA-15THCA
1PEA15Pea-15HNSC
53PEA15PEA15ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
22PIK3R1PI3K-p85ACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THCA,THYM,UCS,UVM
29PIK3R1 PIK3R2PI3K-p85BLCA,BRCA,COAD,GBM,HNSC,KIRC,LUAD,LUSC,OV,READ,SKCM,UCEC
4PIK3R1/2PI3K-p85LGG,PRAD,STAD,THCA
1PRKCA PKC-delta_pS664THCA
54PRKCDPKC-delta_pS664ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,HNSC,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
24PKCPKC-pan_BetaII_pS660ACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
2PRKCA PRKCBPKC-pan_BetaII_pS660THCA
28PRKCBPKC-pan_BetaII_pS660BLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,UCEC
1PKM2KIRC
53PRDX1PRDX1ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
2TRFCPRDX1THCA
1PTCH1PTCHTHCA
1PYGBKIRC
1PYGB-AB2KIRC
1PYGLKIRC
1PYGMKIRC
4Rab 25Rab25LGG,PRAD,STAD,THCA
50RAB25Rab25ACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
2SCDSCD1THCA
24SCD1SCD1ACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
24SFRS1SF2ACC,CESC,CHOL,DLBC,ESCA,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THYM,UCS,UVM
30SRSF1SF2BLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,THCA,UCEC
28SNAI1SnailBLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,UCEC
1SNAI2SnailTHCA
1WWTR1TAZ_pS89THCA
1TFF1TFF1THCA
27C12ORF5TIGARACC,CESC,CHOL,DLBC,ESCA,HNSC,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THCA,THYM,UCS,UVM
28TIGARTIGARBLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,UCEC
53TFRCTFRCACC,BLCA,BRCA,CESC,CHOL,COAD,DLBC,ESCA,GBM,KICH,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,TGCT,THCA,THYM,UCEC,UCS,UVM
2DIRAS3TRFCTHCA
14NKX2-1TTF1BLCA,BRCA,COAD,GBM,KIRC,LUAD,LUSC,OV,READ,SKCM,UCEC
26TTF1TTF1ACC,CESC,CHOL,DLBC,ESCA,HNSC,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,SARC,STAD,TGCT,THCA,THYM,UCS,UVM
1VASPVASPTHCA
1XIAPXIAPTHCA
44Only in 1 cohort
45Same Antibody, different Gene
23Same Gene, suspected typo in antibody

SDRF Issues

Failure in fully processing sdrf file mdanderson.org_BRCA.MDA_RPPA_Core.mage-tab.1.3.0

/xchip/gdac_data/dcc_mirror3/dcc_site/tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/brca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BRCA.MDA_RPPA_Core.mage-tab.1.3.0/mdanderson.org_BRCA.MDA_RPPA_Core.sdrf.txt


protocol mdanderson.org:protein_normalization:01 failed in sdrf file column # 5 
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/SDRFProcessor.py", line 124, in extractFilesFromSDRF
    file_info_bundle = fileBlock.getPerDataFileInfoAndFindUniqueFileBlockSamples()
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/FileBlock.py", line 94, in getPerDataFileInfoAndFindUniqueFileBlockSamples
    "\n\t%s %s %s" % (hyb2tcga_dict[hyb_id],hyb_id,existingFileSubpath))
Exception: Unable to filter conflicting lines in sdrf file:
        TCGA-A1-A0SF-01A-21-A17I-20 f0b3d871-c0aa-4ef8-ab74-c3e812393ed5 ../mdanderson.org_BRCA.MDA_RPPA_Core.Level_3.3.0.0/mdanderson.org_BRCA.MDA_RPPA_Core.protein_expression.Level_3.f0b3d871-c0aa-4ef8-ab74-c3e812393ed5.txt
        TCGA-A1-A0SF-01A-21-A17I-20 f0b3d871-c0aa-4ef8-ab74-c3e812393ed5 ../mdanderson.org_BRCA.MDA_RPPA_Core.Level_3.2.0.0/mdanderson.org_BRCA.MDA_RPPA_Core.protein_expression.Level_3.f0b3d871-c0aa-4ef8-ab74-c3e812393ed5.txt
Failure in fully processing sdrf file mdanderson.org_SKCM.MDA_RPPA_Core.mage-tab.1.6.0

/xchip/gdac_data/dcc_mirror3/dcc_site/tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/skcm/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_SKCM.MDA_RPPA_Core.mage-tab.1.6.0/mdanderson.org_SKCM.MDA_RPPA_Core.sdrf.txt


protocol mdanderson.org:protein_normalization:01 failed in sdrf file column # 5 
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/SDRFProcessor.py", line 124, in extractFilesFromSDRF
    file_info_bundle = fileBlock.getPerDataFileInfoAndFindUniqueFileBlockSamples()
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/FileBlock.py", line 94, in getPerDataFileInfoAndFindUniqueFileBlockSamples
    "\n\t%s %s %s" % (hyb2tcga_dict[hyb_id],hyb_id,existingFileSubpath))
Exception: Unable to filter conflicting lines in sdrf file:
        TCGA-BF-A1PU-01A-21-A20M-20 7E74CAFD-C47B-4F98-A349-BBD2AC699D2D ../mdanderson.org_SKCM.MDA_RPPA_Core.Level_3.2.0.0/mdanderson.org_SKCM.MDA_RPPA_Core.protein_expression.Level_3.7E74CAFD-C47B-4F98-A349-BBD2AC699D2D.txt
        TCGA-BF-A1PU-01A-21-A20M-20 7E74CAFD-C47B-4F98-A349-BBD2AC699D2D ../mdanderson.org_SKCM.MDA_RPPA_Core.Level_3.1.4.0/mdanderson.org_SKCM.MDA_RPPA_Core.protein_expression.Level_3.7E74CAFD-C47B-4F98-A349-BBD2AC699D2D.txt
Fatal error processing sdrf file mdanderson.org_THCA.MDA_RPPA_Core.mage-tab.1.2.0

/xchip/gdac_data/dcc_mirror3/dcc_site/tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_THCA.MDA_RPPA_Core.mage-tab.1.2.0/mdanderson.org_THCA.MDA_RPPA_Core.sdrf.txt


Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/SDRFProcessor.py", line 110, in extractFilesFromSDRF
    fileBlockSamplesDict = self._getFileBlockSamplesDict(headerBlock, dcc_mirror_dirs)
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/SDRFProcessor.py", line 231, in _getFileBlockSamplesDict
    raise Exception(error_msg)
Exception: Protocol REF entry mdanderson.org:antibody_probe:02 is not consistent with prior entry mdanderson.org:antibody_probe:01
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