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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:SOBP-ABCA9

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SOBP-ABCA9
FusionPDB ID: 85061
FusionGDB2.0 ID: 85061
HgeneTgene
Gene symbol

SOBP

ABCA9

Gene ID

55084

10350

Gene namesine oculis binding protein homologATP binding cassette subfamily A member 9
SynonymsJXC1|MRAMSEST640918
Cytomap

6q21

17q24.2

Type of geneprotein-codingprotein-coding
Descriptionsine oculis-binding protein homologjackson circler protein 1ATP-binding cassette sub-family A member 9ATP-binding cassette A9ATP-binding cassette, sub-family A (ABC1), member 9
Modification date2020031320200313
UniProtAcc.

Q8IUA7

Main function of 5'-partner protein: FUNCTION: Transporter that may play a role in monocyte differentiation and lipid transport and homeostasis. {ECO:0000305|PubMed:12150964}.
Ensembl transtripts involved in fusion geneENST idsENST00000317357, ENST00000494935, 
ENST00000482072, ENST00000495634, 
ENST00000340001, ENST00000370732, 
ENST00000453985, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 6 X 6=2886 X 5 X 4=120
# samples 86
** MAII scorelog2(8/288*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SOBP [Title/Abstract] AND ABCA9 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SOBP [Title/Abstract] AND ABCA9 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SOBP(107854814)-ABCA9(67008224), # samples:3
Anticipated loss of major functional domain due to fusion event.SOBP-ABCA9 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.
SOBP-ABCA9 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.
SOBP-ABCA9 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.
SOBP-ABCA9 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


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/chr6:107854814/chr17:67008224)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across SOBP (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 ABCA9 (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 Amino Acid Sequences


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)
ENST00000317357SOBPchr6107854814+ENST00000340001ABCA9chr1767008224-449512326593067802
ENST00000317357SOBPchr6107854814+ENST00000453985ABCA9chr1767008224-423712326592953764
ENST00000317357SOBPchr6107854814+ENST00000370732ABCA9chr1767008224-425512326592500613

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
ENST00000317357ENST00000340001SOBPchr6107854814+ABCA9chr1767008224-0.0005850890.9994149
ENST00000317357ENST00000453985SOBPchr6107854814+ABCA9chr1767008224-0.000999590.9990004
ENST00000317357ENST00000370732SOBPchr6107854814+ABCA9chr1767008224-0.0011028070.9988972

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for SOBP-ABCA9

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SOBPchr6107854814ABCA9chr17670082241232191FAACRRAYFKRNKEHMDYEYGYRSNT

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Potential FusionNeoAntigen Information of SOBP-ABCA9 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
SOBP-ABCA9_107854814_67008224.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
SOBP-ABCA9chr6107854814chr17670082241232HLA-B18:01KEHMDYEY0.99570.95551220
SOBP-ABCA9chr6107854814chr17670082241232HLA-B27:02KRNKEHMDY0.99780.6358918
SOBP-ABCA9chr6107854814chr17670082241232HLA-B27:05KRNKEHMDY0.99760.91918
SOBP-ABCA9chr6107854814chr17670082241232HLA-B27:04KRNKEHMDY0.99660.7228918
SOBP-ABCA9chr6107854814chr17670082241232HLA-B44:03KEHMDYEYGY0.99930.78191222
SOBP-ABCA9chr6107854814chr17670082241232HLA-B27:02KRNKEHMDYEY0.99990.7077920
SOBP-ABCA9chr6107854814chr17670082241232HLA-B27:03KRNKEHMDY0.97380.928918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:95KRNKEHMDY0.96660.7558918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:27KRNKEHMDY0.86710.9549918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:05KRNKEHMDY0.82230.9507918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:19KRNKEHMDY0.81860.8067918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:80KRNKEHMDY0.70790.9507918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:67KRNKEHMDY0.70790.9507918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:10KRNKEHMDY0.70750.961918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:46KRNKEHMDY0.67060.9113918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C12:16KRNKEHMDY0.00840.9424918
SOBP-ABCA9chr6107854814chr17670082241232HLA-B27:03KRNKEHMDYEY0.9980.9409920
SOBP-ABCA9chr6107854814chr17670082241232HLA-B18:11KEHMDYEY0.99730.9051220
SOBP-ABCA9chr6107854814chr17670082241232HLA-B18:06KEHMDYEY0.99570.95461220
SOBP-ABCA9chr6107854814chr17670082241232HLA-B18:05KEHMDYEY0.99570.95551220
SOBP-ABCA9chr6107854814chr17670082241232HLA-B27:08KRNKEHMDY0.99750.804918
SOBP-ABCA9chr6107854814chr17670082241232HLA-B27:10KRNKEHMDY0.99630.8714918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:01KRNKEHMDY0.97610.7346918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:17KRNKEHMDY0.81670.9554918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:22KRNKEHMDY0.72740.7143918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C07:02KRNKEHMDY0.70790.9507918
SOBP-ABCA9chr6107854814chr17670082241232HLA-C14:02YFKRNKEHM0.17050.9334716
SOBP-ABCA9chr6107854814chr17670082241232HLA-C14:03YFKRNKEHM0.17050.9334716
SOBP-ABCA9chr6107854814chr17670082241232HLA-C03:67YFKRNKEHM0.11580.9577716
SOBP-ABCA9chr6107854814chr17670082241232HLA-C06:06YFKRNKEHM0.06690.9803716
SOBP-ABCA9chr6107854814chr17670082241232HLA-B15:68KRNKEHMDY0.00330.6929918
SOBP-ABCA9chr6107854814chr17670082241232HLA-B44:13KEHMDYEYGY0.99930.78191222
SOBP-ABCA9chr6107854814chr17670082241232HLA-B44:07KEHMDYEYGY0.99930.78191222
SOBP-ABCA9chr6107854814chr17670082241232HLA-B44:26KEHMDYEYGY0.99930.78191222
SOBP-ABCA9chr6107854814chr17670082241232HLA-B48:02KEHMDYEYGY0.89680.70351222

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Potential FusionNeoAntigen Information of SOBP-ABCA9 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
SOBP-ABCA9_107854814_67008224.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
SOBP-ABCA9chr6107854814chr17670082241232DRB1-1338RRAYFKRNKEHMDYE419
SOBP-ABCA9chr6107854814chr17670082241232DRB1-1338RAYFKRNKEHMDYEY520
SOBP-ABCA9chr6107854814chr17670082241232DRB1-1365RRAYFKRNKEHMDYE419
SOBP-ABCA9chr6107854814chr17670082241232DRB1-1365RAYFKRNKEHMDYEY520

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Fusion breakpoint peptide structures of SOBP-ABCA9

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
735AYFKRNKEHMDYEYSOBPABCA9chr6107854814chr17670082241232

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SOBP-ABCA9

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN735AYFKRNKEHMDYEY-7.15543-7.26883
HLA-B14:023BVN735AYFKRNKEHMDYEY-4.77435-5.80965
HLA-B52:013W39735AYFKRNKEHMDYEY-6.80875-6.92215
HLA-B52:013W39735AYFKRNKEHMDYEY-4.20386-5.23916
HLA-A11:014UQ2735AYFKRNKEHMDYEY-7.5194-8.5547
HLA-A11:014UQ2735AYFKRNKEHMDYEY-6.9601-7.0735
HLA-A24:025HGA735AYFKRNKEHMDYEY-7.52403-7.63743
HLA-A24:025HGA735AYFKRNKEHMDYEY-5.82433-6.85963
HLA-B27:056PYJ735AYFKRNKEHMDYEY-3.28285-4.31815
HLA-B44:053DX8735AYFKRNKEHMDYEY-5.91172-6.94702
HLA-B44:053DX8735AYFKRNKEHMDYEY-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of SOBP-ABCA9

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
SOBP-ABCA9chr6107854814chr17670082241220KEHMDYEYAAGGAGCATATGGATTATGAGTAT
SOBP-ABCA9chr6107854814chr17670082241222KEHMDYEYGYAAGGAGCATATGGATTATGAGTATGGGTAC
SOBP-ABCA9chr6107854814chr1767008224716YFKRNKEHMTACTTCAAGAGAAATAAGGAGCATATG
SOBP-ABCA9chr6107854814chr1767008224918KRNKEHMDYAAGAGAAATAAGGAGCATATGGATTAT
SOBP-ABCA9chr6107854814chr1767008224920KRNKEHMDYEYAAGAGAAATAAGGAGCATATGGATTATGAGTAT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
SOBP-ABCA9chr6107854814chr1767008224419RRAYFKRNKEHMDYECGACGAGCCTACTTCAAGAGAAATAAGGAGCATATGGATTATGAG
SOBP-ABCA9chr6107854814chr1767008224520RAYFKRNKEHMDYEYCGAGCCTACTTCAAGAGAAATAAGGAGCATATGGATTATGAGTAT

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Information of the samples that have these potential fusion neoantigens of SOBP-ABCA9

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample
BRCASOBP-ABCA9chr6107854814ENST00000317357chr1767008224ENST00000340001TCGA-D8-A147-01A

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Potential target of CAR-T therapy development for SOBP-ABCA9

check button Predicted 3D structure. We used RoseTTAFold.
466_SOBP-ABCA9_t000_.e2e.pdb


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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneABCA9chr6:107854814chr17:67008224ENST0000034000121391026_104601625.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000034000121391065_108501625.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000034000121391108_112801625.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000034000121391136_115601625.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000034000121391163_118301625.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000034000121391200_122001625.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000037073221381026_104601790.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000037073221381065_108501790.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000037073221381108_112801790.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000037073221381136_115601790.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000037073221381163_118301790.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000037073221381200_122001790.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST00000495634061026_10460268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST00000495634061065_10850268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST00000495634061108_11280268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST00000495634061136_11560268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST00000495634061163_11830268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST00000495634061200_12200268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000049563406221_2430268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000049563406269_2890268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000049563406300_3200268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST000004956340631_510268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000049563406329_3490268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000049563406354_3740268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000049563406398_4180268.0TransmembraneHelical
TgeneABCA9chr6:107854814chr17:67008224ENST0000049563406864_8840268.0TransmembraneHelical

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result
SOBPchr6107854814ENST00000317357ABCA9chr1767008224ENST00000340001
SOBPchr6107854814ENST00000317357ABCA9chr1767008224ENST00000370732
SOBPchr6107854814ENST00000317357ABCA9chr1767008224ENST00000453985

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Related Drugs to SOBP-ABCA9

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 SOBP-ABCA9

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