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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:KDM5A-RAE1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KDM5A-RAE1
FusionPDB ID: 41856
FusionGDB2.0 ID: 41856
HgeneTgene
Gene symbol

KDM5A

RAE1

Gene ID

5927

84659

Gene namelysine demethylase 5Aribonuclease A family member 7
SynonymsRBBP-2|RBBP2|RBP2RAE1
Cytomap

12p13.33

14q11.2

Type of geneprotein-codingprotein-coding
Descriptionlysine-specific demethylase 5AJumonji, AT rich interactive domain 1A (RBP2-like)histone demethylase JARID1Ajumonji/ARID domain-containing protein 1Alysine (K)-specific demethylase 5Aretinoblastoma binding protein 2ribonuclease 7RNase 7SAP-2ribonuclease, RNase A family, 7skin-derived antimicrobial protein 2
Modification date2020031320200313
UniProtAcc

P29375

.
Ensembl transtripts involved in fusion geneENST idsENST00000382815, ENST00000399788, 
ENST00000540838, 
ENST00000371242, 
ENST00000395840, ENST00000395841, 
ENST00000527947, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 15 X 6=9909 X 11 X 5=495
# samples 1810
** MAII scorelog2(18/990*10)=-2.4594316186373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/495*10)=-2.30742852519225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: KDM5A [Title/Abstract] AND RAE1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KDM5A(459787)-RAE1(55940412), # samples:3
Anticipated loss of major functional domain due to fusion event.KDM5A-RAE1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
KDM5A-RAE1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
KDM5A-RAE1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
KDM5A-RAE1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneKDM5A

GO:0034720

histone H3-K4 demethylation

18270511

HgeneKDM5A

GO:0045893

positive regulation of transcription, DNA-templated

11358960

TgeneRAE1

GO:0019731

antibacterial humoral response

23302724|25075772

TgeneRAE1

GO:0045087

innate immune response

16940129|23302724|25075772

TgeneRAE1

GO:0050829

defense response to Gram-negative bacterium

12244054|16940129|20180804|23302724|25075772

TgeneRAE1

GO:0050830

defense response to Gram-positive bacterium

12244054|16940129|19641608|20180804|23302724|25075772

TgeneRAE1

GO:0050832

defense response to fungus

12244054

TgeneRAE1

GO:0051673

membrane disruption in other organism

20180804|23302724

TgeneRAE1

GO:0061844

antimicrobial humoral immune response mediated by antimicrobial peptide

12244054|25075772


check buttonFusion gene breakpoints across KDM5A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across RAE1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LUADTCGA-44-A47B-01AKDM5Achr12

459787

-RAE1chr20

55940412

+
ChimerDB4LUADTCGA-44-A47BKDM5Achr12

459786

-RAE1chr20

55940411

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000399788KDM5Achr12459787-ENST00000395841RAE1chr2055940412+360216713632489708
ENST00000399788KDM5Achr12459787-ENST00000371242RAE1chr2055940412+360216713632489708
ENST00000399788KDM5Achr12459787-ENST00000527947RAE1chr2055940412+270816713632696777
ENST00000399788KDM5Achr12459787-ENST00000395840RAE1chr2055940412+360216713632489708
ENST00000382815KDM5Achr12459787-ENST00000395841RAE1chr2055940412+360216713632489708
ENST00000382815KDM5Achr12459787-ENST00000371242RAE1chr2055940412+360216713632489708
ENST00000382815KDM5Achr12459787-ENST00000527947RAE1chr2055940412+270816713632696777
ENST00000382815KDM5Achr12459787-ENST00000395840RAE1chr2055940412+360216713632489708
ENST00000399788KDM5Achr12459786-ENST00000395841RAE1chr2055940411+360216713632489708
ENST00000399788KDM5Achr12459786-ENST00000371242RAE1chr2055940411+360216713632489708
ENST00000399788KDM5Achr12459786-ENST00000527947RAE1chr2055940411+270816713632696777
ENST00000399788KDM5Achr12459786-ENST00000395840RAE1chr2055940411+360216713632489708
ENST00000382815KDM5Achr12459786-ENST00000395841RAE1chr2055940411+360216713632489708
ENST00000382815KDM5Achr12459786-ENST00000371242RAE1chr2055940411+360216713632489708
ENST00000382815KDM5Achr12459786-ENST00000527947RAE1chr2055940411+270816713632696777
ENST00000382815KDM5Achr12459786-ENST00000395840RAE1chr2055940411+360216713632489708

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000399788ENST00000395841KDM5Achr12459787-RAE1chr2055940412+0.0013776450.9986224
ENST00000399788ENST00000371242KDM5Achr12459787-RAE1chr2055940412+0.0013776450.9986224
ENST00000399788ENST00000527947KDM5Achr12459787-RAE1chr2055940412+0.0024731410.9975268
ENST00000399788ENST00000395840KDM5Achr12459787-RAE1chr2055940412+0.0013776450.9986224
ENST00000382815ENST00000395841KDM5Achr12459787-RAE1chr2055940412+0.0013776450.9986224
ENST00000382815ENST00000371242KDM5Achr12459787-RAE1chr2055940412+0.0013776450.9986224
ENST00000382815ENST00000527947KDM5Achr12459787-RAE1chr2055940412+0.0024731410.9975268
ENST00000382815ENST00000395840KDM5Achr12459787-RAE1chr2055940412+0.0013776450.9986224
ENST00000399788ENST00000395841KDM5Achr12459786-RAE1chr2055940411+0.0013776450.9986224
ENST00000399788ENST00000371242KDM5Achr12459786-RAE1chr2055940411+0.0013776450.9986224
ENST00000399788ENST00000527947KDM5Achr12459786-RAE1chr2055940411+0.0024731410.9975268
ENST00000399788ENST00000395840KDM5Achr12459786-RAE1chr2055940411+0.0013776450.9986224
ENST00000382815ENST00000395841KDM5Achr12459786-RAE1chr2055940411+0.0013776450.9986224
ENST00000382815ENST00000371242KDM5Achr12459786-RAE1chr2055940411+0.0013776450.9986224
ENST00000382815ENST00000527947KDM5Achr12459786-RAE1chr2055940411+0.0024731410.9975268
ENST00000382815ENST00000395840KDM5Achr12459786-RAE1chr2055940411+0.0013776450.9986224

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>41856_41856_1_KDM5A-RAE1_KDM5A_chr12_459786_ENST00000382815_RAE1_chr20_55940411_ENST00000371242_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_2_KDM5A-RAE1_KDM5A_chr12_459786_ENST00000382815_RAE1_chr20_55940411_ENST00000395840_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_3_KDM5A-RAE1_KDM5A_chr12_459786_ENST00000382815_RAE1_chr20_55940411_ENST00000395841_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_4_KDM5A-RAE1_KDM5A_chr12_459786_ENST00000382815_RAE1_chr20_55940411_ENST00000527947_length(amino acids)=777AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT
VGSDGRFSFWDKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKVRTPGPALGAPRQQSQALGSEGLGLSCDSSQDSRVSLGRS

--------------------------------------------------------------

>41856_41856_5_KDM5A-RAE1_KDM5A_chr12_459786_ENST00000399788_RAE1_chr20_55940411_ENST00000371242_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_6_KDM5A-RAE1_KDM5A_chr12_459786_ENST00000399788_RAE1_chr20_55940411_ENST00000395840_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_7_KDM5A-RAE1_KDM5A_chr12_459786_ENST00000399788_RAE1_chr20_55940411_ENST00000395841_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_8_KDM5A-RAE1_KDM5A_chr12_459786_ENST00000399788_RAE1_chr20_55940411_ENST00000527947_length(amino acids)=777AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT
VGSDGRFSFWDKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKVRTPGPALGAPRQQSQALGSEGLGLSCDSSQDSRVSLGRS

--------------------------------------------------------------

>41856_41856_9_KDM5A-RAE1_KDM5A_chr12_459787_ENST00000382815_RAE1_chr20_55940412_ENST00000371242_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_10_KDM5A-RAE1_KDM5A_chr12_459787_ENST00000382815_RAE1_chr20_55940412_ENST00000395840_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_11_KDM5A-RAE1_KDM5A_chr12_459787_ENST00000382815_RAE1_chr20_55940412_ENST00000395841_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_12_KDM5A-RAE1_KDM5A_chr12_459787_ENST00000382815_RAE1_chr20_55940412_ENST00000527947_length(amino acids)=777AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT
VGSDGRFSFWDKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKVRTPGPALGAPRQQSQALGSEGLGLSCDSSQDSRVSLGRS

--------------------------------------------------------------

>41856_41856_13_KDM5A-RAE1_KDM5A_chr12_459787_ENST00000399788_RAE1_chr20_55940412_ENST00000371242_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_14_KDM5A-RAE1_KDM5A_chr12_459787_ENST00000399788_RAE1_chr20_55940412_ENST00000395840_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_15_KDM5A-RAE1_KDM5A_chr12_459787_ENST00000399788_RAE1_chr20_55940412_ENST00000395841_length(amino acids)=708AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT

--------------------------------------------------------------

>41856_41856_16_KDM5A-RAE1_KDM5A_chr12_459787_ENST00000399788_RAE1_chr20_55940412_ENST00000527947_length(amino acids)=777AA_BP=426
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRLDF
LDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYELFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTKDKEDEVTRRRKVTN
RSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEDGSKVFTASCDKTA
KMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQ
PSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLAT
VGSDGRFSFWDKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKVRTPGPALGAPRQQSQALGSEGLGLSCDSSQDSRVSLGRS

--------------------------------------------------------------

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:459787/chr20:55940412)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KDM5A

P29375

.
FUNCTION: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Regulates specific gene transcription through DNA-binding on 5'-CCGCCC-3' motif (PubMed:18270511). May stimulate transcription mediated by nuclear receptors. Involved in transcriptional regulation of Hox proteins during cell differentiation (PubMed:19430464). May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1 (By similarity). Seems to act as a transcriptional corepressor for some genes such as MT1F and to favor the proliferation of cancer cells (PubMed:27427228). {ECO:0000250|UniProtKB:Q3UXZ9, ECO:0000269|PubMed:11358960, ECO:0000269|PubMed:15949438, ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17320163, ECO:0000269|PubMed:18270511, ECO:0000269|PubMed:19430464, ECO:0000269|PubMed:27427228}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-102819_60436.01691.0DomainJmjN
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-102884_174436.01691.0DomainARID
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-102819_60436.01691.0DomainJmjN
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-102884_174436.01691.0DomainARID
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-1028419_423436.01691.0MotifGSGFP motif
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-1028419_423436.01691.0MotifGSGFP motif
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-1028293_343436.01691.0Zinc fingerPHD-type 1
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-1028293_343436.01691.0Zinc fingerPHD-type 1
TgeneRAE1chr12:459786chr20:55940411ENST00000371242312125_15796.0369.0RepeatWD 3
TgeneRAE1chr12:459786chr20:55940411ENST00000371242312168_20696.0369.0RepeatWD 4
TgeneRAE1chr12:459786chr20:55940411ENST00000371242312215_25596.0369.0RepeatWD 5
TgeneRAE1chr12:459786chr20:55940411ENST00000371242312271_30196.0369.0RepeatWD 6
TgeneRAE1chr12:459786chr20:55940411ENST00000371242312310_34696.0369.0RepeatWD 7
TgeneRAE1chr12:459786chr20:55940411ENST00000395840312125_15796.0369.0RepeatWD 3
TgeneRAE1chr12:459786chr20:55940411ENST00000395840312168_20696.0369.0RepeatWD 4
TgeneRAE1chr12:459786chr20:55940411ENST00000395840312215_25596.0369.0RepeatWD 5
TgeneRAE1chr12:459786chr20:55940411ENST00000395840312271_30196.0369.0RepeatWD 6
TgeneRAE1chr12:459786chr20:55940411ENST00000395840312310_34696.0369.0RepeatWD 7
TgeneRAE1chr12:459786chr20:55940411ENST00000395841312125_15796.0369.0RepeatWD 3
TgeneRAE1chr12:459786chr20:55940411ENST00000395841312168_20696.0369.0RepeatWD 4
TgeneRAE1chr12:459786chr20:55940411ENST00000395841312215_25596.0369.0RepeatWD 5
TgeneRAE1chr12:459786chr20:55940411ENST00000395841312271_30196.0369.0RepeatWD 6
TgeneRAE1chr12:459786chr20:55940411ENST00000395841312310_34696.0369.0RepeatWD 7
TgeneRAE1chr12:459787chr20:55940412ENST00000371242312125_15796.0369.0RepeatWD 3
TgeneRAE1chr12:459787chr20:55940412ENST00000371242312168_20696.0369.0RepeatWD 4
TgeneRAE1chr12:459787chr20:55940412ENST00000371242312215_25596.0369.0RepeatWD 5
TgeneRAE1chr12:459787chr20:55940412ENST00000371242312271_30196.0369.0RepeatWD 6
TgeneRAE1chr12:459787chr20:55940412ENST00000371242312310_34696.0369.0RepeatWD 7
TgeneRAE1chr12:459787chr20:55940412ENST00000395840312125_15796.0369.0RepeatWD 3
TgeneRAE1chr12:459787chr20:55940412ENST00000395840312168_20696.0369.0RepeatWD 4
TgeneRAE1chr12:459787chr20:55940412ENST00000395840312215_25596.0369.0RepeatWD 5
TgeneRAE1chr12:459787chr20:55940412ENST00000395840312271_30196.0369.0RepeatWD 6
TgeneRAE1chr12:459787chr20:55940412ENST00000395840312310_34696.0369.0RepeatWD 7
TgeneRAE1chr12:459787chr20:55940412ENST00000395841312125_15796.0369.0RepeatWD 3
TgeneRAE1chr12:459787chr20:55940412ENST00000395841312168_20696.0369.0RepeatWD 4
TgeneRAE1chr12:459787chr20:55940412ENST00000395841312215_25596.0369.0RepeatWD 5
TgeneRAE1chr12:459787chr20:55940412ENST00000395841312271_30196.0369.0RepeatWD 6
TgeneRAE1chr12:459787chr20:55940412ENST00000395841312310_34696.0369.0RepeatWD 7

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-10281492_1587436.01691.0Compositional biasNote=Lys-rich
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-10281492_1587436.01691.0Compositional biasNote=Lys-rich
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-1028437_603436.01691.0DomainJmjC
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-1028437_603436.01691.0DomainJmjC
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-10281161_1218436.01691.0Zinc fingerPHD-type 2
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-10281607_1661436.01691.0Zinc fingerPHD-type 3
HgeneKDM5Achr12:459786chr20:55940411ENST00000399788-1028676_728436.01691.0Zinc fingerC5HC2
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-10281161_1218436.01691.0Zinc fingerPHD-type 2
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-10281607_1661436.01691.0Zinc fingerPHD-type 3
HgeneKDM5Achr12:459787chr20:55940412ENST00000399788-1028676_728436.01691.0Zinc fingerC5HC2
TgeneRAE1chr12:459786chr20:55940411ENST0000037124231237_7996.0369.0RepeatWD 1
TgeneRAE1chr12:459786chr20:55940411ENST0000037124231284_11496.0369.0RepeatWD 2
TgeneRAE1chr12:459786chr20:55940411ENST0000039584031237_7996.0369.0RepeatWD 1
TgeneRAE1chr12:459786chr20:55940411ENST0000039584031284_11496.0369.0RepeatWD 2
TgeneRAE1chr12:459786chr20:55940411ENST0000039584131237_7996.0369.0RepeatWD 1
TgeneRAE1chr12:459786chr20:55940411ENST0000039584131284_11496.0369.0RepeatWD 2
TgeneRAE1chr12:459787chr20:55940412ENST0000037124231237_7996.0369.0RepeatWD 1
TgeneRAE1chr12:459787chr20:55940412ENST0000037124231284_11496.0369.0RepeatWD 2
TgeneRAE1chr12:459787chr20:55940412ENST0000039584031237_7996.0369.0RepeatWD 1
TgeneRAE1chr12:459787chr20:55940412ENST0000039584031284_11496.0369.0RepeatWD 2
TgeneRAE1chr12:459787chr20:55940412ENST0000039584131237_7996.0369.0RepeatWD 1
TgeneRAE1chr12:459787chr20:55940412ENST0000039584131284_11496.0369.0RepeatWD 2


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Fusion Protein-Protein Interaction


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
KDM5A
RAE1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to KDM5A-RAE1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to KDM5A-RAE1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource