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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:PGA3-PGC

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PGA3-PGC
FusionPDB ID: 64507
FusionGDB2.0 ID: 64507
HgeneTgene
Gene symbol

PGA3

PGC

Gene ID

643834

5225

Gene namepepsinogen A3progastricsin
Synonyms-PEPC|PGII
Cytomap

11q12.2

6p21.1

Type of geneprotein-codingprotein-coding
Descriptionpepsin A-3pepsinogen 3, group I (pepsinogen A)pepsinogen-3gastricsinpepsin Cpepsinogen Cpepsinogen group IIpreprogastricsin
Modification date2020031320200313
UniProtAcc.

PERM1

Ensembl transtripts involved in fusion geneENST idsENST00000325558, ENST00000538258, 
ENST00000543125, 
ENST00000425343, 
ENST00000373025, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 13 X 4=78024 X 21 X 8=4032
# samples 1625
** MAII scorelog2(16/780*10)=-2.28540221886225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(25/4032*10)=-4.01149563883783
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PGA3 [Title/Abstract] AND PGC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PGA3(60974099)-PGC(41711127), # samples:18
PGC(41710027)-PGA3(60977313), # samples:13
Anticipated loss of major functional domain due to fusion event.PGA3-PGC 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.
PGA3-PGC 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.
PGA3-PGC 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.
PGA3-PGC 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.
PGC-PGA3 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.
PGC-PGA3 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.
PGA3-PGC seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PGA3-PGC seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PGC-PGA3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PGC-PGA3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted 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

check buttonFusion gene breakpoints across PGA3 (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 PGC (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
ChimerDB4Non-Cancer115NdPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer115NdPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer115NdPGA3chr11

60974099

+PGCchr6

41712252

-
ChimerDB4Non-Cancer115NdPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer115NdPGA3chr11

60978907

+PGCchr6

41704742

-
ChimerDB4Non-Cancer117NdPGA3chr11

60971741

+PGCchr6

41705566

-
ChimerDB4Non-Cancer117NdPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer117NdPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer117NdPGA3chr11

60978907

+PGCchr6

41711127

-
ChimerDB4Non-Cancer119NdPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer119NdPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer119NdPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer123NdPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer123NdPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer123NdPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer123NdPGA3chr11

60978907

+PGCchr6

41704742

-
ChimerDB4Non-Cancer131NdPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer131NdPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer131NdPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer139NPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer139NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer145NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer203NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer203NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer217NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer217NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer231NPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer231NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer231NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer2397NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer267NPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer267NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer267NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer5263NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer5263NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer5357NPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer5357NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer5357NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer5381NPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer5381NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer5381NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-Cancer5759NPGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-Cancer5759NPGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-Cancer5759NPGA3chr11

60975962

+PGCchr6

41708348

-
ChimerDB4Non-CancerTCGA-BR-6458-11APGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-CancerTCGA-BR-6458-11APGA3chr11

60997445

+PGCchr6

41707626

-
ChimerDB4Non-CancerTCGA-BR-8060-11APGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-CancerTCGA-L5-A43C-11APGA3chr11

60971741

+PGCchr6

41705566

-
ChimerDB4Non-CancerTCGA-L5-A43C-11APGA3chr11

60971741

+PGCchr6

41712252

-
ChimerDB4Non-CancerTCGA-L5-A43C-11APGA3chr11

60974099

+PGCchr6

41711127

-
ChimerDB4Non-CancerTCGA-L5-A4OG-11APGA3chr11

60974099

+PGCchr6

41711127

-


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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)
ENST00000325558PGA3chr1160971741+ENST00000373025PGCchr641705566-79740456232176
ENST00000325558PGA3chr1160974099+ENST00000373025PGCchr641711127-15025221311360409
ENST00000325558PGA3chr1160974099+ENST00000425343PGCchr641711127-12795221311141336
ENST00000325558PGA3chr1160971741+ENST00000373025PGCchr641712252-1502404126732411
ENST00000325558PGA3chr1160971741+ENST00000425343PGCchr641712252-12794041311141336
ENST00000325558PGA3chr1160975962+ENST00000373025PGCchr641708348-15028411311360409

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
ENST00000325558ENST00000373025PGA3chr1160971741+PGCchr641705566-0.0271894930.9728105
ENST00000325558ENST00000373025PGA3chr1160974099+PGCchr641711127-0.0070719470.9929281
ENST00000325558ENST00000425343PGA3chr1160974099+PGCchr641711127-0.041793590.95820636
ENST00000325558ENST00000373025PGA3chr1160971741+PGCchr641712252-0.0083839250.9916161
ENST00000325558ENST00000425343PGA3chr1160971741+PGCchr641712252-0.0415520220.958448
ENST00000325558ENST00000373025PGA3chr1160975962+PGCchr641708348-0.0055300780.9944699

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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

>64507_64507_1_PGA3-PGC_PGA3_chr11_60971741_ENST00000325558_PGC_chr6_41705566_ENST00000373025_length(amino acids)=176AA_BP=1
MAVLGGQVGGLDSHGAVAVVTEDIGGRWQRELHTIDDEGQAGQILNAVTVHEKIQVVLQGLFIYQGGSLPLGEVLSGWVEVVLLQEVLQQ

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

>64507_64507_2_PGA3-PGC_PGA3_chr11_60971741_ENST00000325558_PGC_chr6_41712252_ENST00000373025_length(amino acids)=411AA_BP=1
MAVLGGQVGGLDSHGAVAVVTEDIGGRWQRELHTIDDEGQAGQILNAVTVHEKLSILILLGPCGLQKSTHVLLGHSEQRGACVHDGLATL
RTPAGGLAADEELFNANLPVEFLGDRRPVDLPRVQAAIHTPKDNRSPAGALLVAEVDAEDGAGEGALLHHALHSCGGLIHGQSRVGQAHD
AIKLRIDEVGTRLILTQAELLVGDLDALDSQGVIAKEAGEAATAILQGEGLPIGGVGGRLAGVEAGVTGAGLALAVDRGHPQVGGAGVKK
DQEVLGWSPDADLTKVGSIQVVLQGLFIYQGGSLPLGEVLSGWVEVVLLQEVLQQATLGQGAPQGLLSDEGDLVHDALRECHQTQQQQPL

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

>64507_64507_3_PGA3-PGC_PGA3_chr11_60971741_ENST00000325558_PGC_chr6_41712252_ENST00000425343_length(amino acids)=336AA_BP=91
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DAAYFGEISIGTPPQNFLVLFDTGSSNLWVPSVYCQSQACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQE
FGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSNLVLESSGLGPLLTPSRAAPPSSTLQLPEKPLEQ

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

>64507_64507_4_PGA3-PGC_PGA3_chr11_60974099_ENST00000325558_PGC_chr6_41711127_ENST00000373025_length(amino acids)=409AA_BP=93
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQE
FGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSNQQGSSGGAVVFGGVDSSLYTGQIYWAPVTQELY
WQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSN

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

>64507_64507_5_PGA3-PGC_PGA3_chr11_60974099_ENST00000325558_PGC_chr6_41711127_ENST00000425343_length(amino acids)=336AA_BP=93
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQE
FGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSNLVLESSGLGPLLTPSRAAPPSSTLQLPEKPLEQ

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

>64507_64507_6_PGA3-PGC_PGA3_chr11_60975962_ENST00000325558_PGC_chr6_41708348_ENST00000373025_length(amino acids)=409AA_BP=93
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTNHNRFNPEDSSTYQSTSETVSITYGTGSMTGILGYDTVQVGGISDTNQI
FGLSETEPGSFLYYAPFDGILGLAYPSISSSGATPVFDNIWNQGLVSQDLFSVYLSAQQGSSGGAVVFGGVDSSLYTGQIYWAPVTQELY
WQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSN

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

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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/chr11:60974099/chr6:41711127)
- 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
.PGC

PERM1

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.790

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
TgenePGCchr11:60971741chr6:41705566ENST000004253430773_3850316.0DomainPeptidase A1
TgenePGCchr11:60971741chr6:41712252ENST000003730251973_38570.0389.0DomainPeptidase A1
TgenePGCchr11:60971741chr6:41712252ENST000004253431773_38570.0316.0DomainPeptidase A1
TgenePGCchr11:60975962chr6:41708348ENST000004253430773_3850316.0DomainPeptidase A1

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePGA3chr11:60971741chr6:41705566ENST00000325558+2976_38573.0389.0DomainPeptidase A1
HgenePGA3chr11:60971741chr6:41712252ENST00000325558+2976_38573.0389.0DomainPeptidase A1
HgenePGA3chr11:60974099chr6:41711127ENST00000325558+3976_385112.33333333333333389.0DomainPeptidase A1
HgenePGA3chr11:60975962chr6:41708348ENST00000325558+5976_385218.66666666666666389.0DomainPeptidase A1
TgenePGCchr11:60971741chr6:41705566ENST000003730256973_385305.0389.0DomainPeptidase A1
TgenePGCchr11:60974099chr6:41711127ENST000003730252973_385109.33333333333333389.0DomainPeptidase A1
TgenePGCchr11:60974099chr6:41711127ENST000004253432773_385109.33333333333333316.0DomainPeptidase A1
TgenePGCchr11:60975962chr6:41708348ENST000003730254973_385215.66666666666666389.0DomainPeptidase A1


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>832_PGA3_60974099_PGC_41711127_832_PGA3_60974099_PGC_41711127_ranked_0.pdbPGA36097596260974099ENST00000373025PGCchr641711127-
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQE
FGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSNQQGSSGGAVVFGGVDSSLYTGQIYWAPVTQELY
WQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSN
409


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
PGA3_pLDDT.png
all structure
all structure
PGC_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
PGA3
PGC


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 PGA3-PGC


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 PGA3-PGC


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