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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:FAM60A-MADCAM1 (FusionGDB2 ID:29038)

Fusion Gene Summary for FAM60A-MADCAM1

check button Fusion gene summary
Fusion gene informationFusion gene name: FAM60A-MADCAM1
Fusion gene ID: 29038
HgeneTgene
Gene symbol

FAM60A

MADCAM1

Gene ID

58516

8174

Gene nameSIN3-HDAC complex associated factormucosal vascular addressin cell adhesion molecule 1
SynonymsC12orf14|FAM60A|L4|TERAMACAM1
Cytomap

12p11.21

19p13.3

Type of geneprotein-codingprotein-coding
DescriptionSIN3-HDAC complex-associated factorfamily with sequence similarity 60 member Aprotein FAM60Atera protein homologmucosal addressin cell adhesion molecule 1MAdCAM-1hMAdCAM-1
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000539409, ENST00000337682, 
ENST00000454658, ENST00000395766, 
ENST00000542983, ENST00000536836, 
ENST00000587541, ENST00000215637, 
ENST00000346144, ENST00000382683, 
Fusion gene scores* DoF score11 X 5 X 8=4402 X 3 X 2=12
# samples 134
** MAII scorelog2(13/440*10)=-1.7589919004962
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/12*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: FAM60A [Title/Abstract] AND MADCAM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFAM60A(31478958)-MADCAM1(501669), # samples:2
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneMADCAM1

GO:0007160

cell-matrix adhesion

18308860

TgeneMADCAM1

GO:0007229

integrin-mediated signaling pathway

23986478

TgeneMADCAM1

GO:0043113

receptor clustering

23986478

TgeneMADCAM1

GO:0050901

leukocyte tethering or rolling

18308860


check buttonFusion gene breakpoints across FAM60A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across MADCAM1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4STADTCGA-CD-8525-01AFAM60Achr12

31478958

-MADCAM1chr19

501669

+
ChimerDB4STADTCGA-CD-8525FAM60Achr12

31478957

-MADCAM1chr19

501668

+
ChimerDB4STADTCGA-CD-8525-01AFAM60Achr12

31478958

-MADCAM1chr19

501669

+
ChimerDB4STADTCGA-CD-8525-01AFAM60Achr12

31478960

-MADCAM1chr19

501667

+


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Fusion Gene ORF analysis for FAM60A-MADCAM1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5UTR-3CDSENST00000539409ENST00000587541FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000539409ENST00000215637FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000539409ENST00000346144FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000539409ENST00000382683FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000337682ENST00000587541FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000337682ENST00000215637FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000337682ENST00000346144FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000337682ENST00000382683FAM60Achr12

31478958

-MADCAM1chr19

501669

+
intron-3CDSENST00000454658ENST00000587541FAM60Achr12

31478958

-MADCAM1chr19

501669

+
intron-3CDSENST00000454658ENST00000215637FAM60Achr12

31478958

-MADCAM1chr19

501669

+
intron-intronENST00000454658ENST00000346144FAM60Achr12

31478958

-MADCAM1chr19

501669

+
intron-intronENST00000454658ENST00000382683FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000395766ENST00000587541FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000395766ENST00000215637FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000395766ENST00000346144FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000395766ENST00000382683FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000542983ENST00000587541FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000542983ENST00000215637FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000542983ENST00000346144FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000542983ENST00000382683FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000536836ENST00000587541FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000536836ENST00000215637FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000536836ENST00000346144FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-intronENST00000536836ENST00000382683FAM60Achr12

31478958

-MADCAM1chr19

501669

+
5UTR-3CDSENST00000539409ENST00000587541FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000539409ENST00000215637FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000539409ENST00000346144FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000539409ENST00000382683FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000337682ENST00000587541FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000337682ENST00000215637FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000337682ENST00000346144FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000337682ENST00000382683FAM60Achr12

31478957

-MADCAM1chr19

501668

+
intron-3CDSENST00000454658ENST00000587541FAM60Achr12

31478957

-MADCAM1chr19

501668

+
intron-3CDSENST00000454658ENST00000215637FAM60Achr12

31478957

-MADCAM1chr19

501668

+
intron-intronENST00000454658ENST00000346144FAM60Achr12

31478957

-MADCAM1chr19

501668

+
intron-intronENST00000454658ENST00000382683FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000395766ENST00000587541FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000395766ENST00000215637FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000395766ENST00000346144FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000395766ENST00000382683FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000542983ENST00000587541FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000542983ENST00000215637FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000542983ENST00000346144FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000542983ENST00000382683FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000536836ENST00000587541FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000536836ENST00000215637FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000536836ENST00000346144FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-intronENST00000536836ENST00000382683FAM60Achr12

31478957

-MADCAM1chr19

501668

+
5UTR-3CDSENST00000539409ENST00000587541FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000539409ENST00000215637FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000539409ENST00000346144FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000539409ENST00000382683FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000337682ENST00000587541FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000337682ENST00000215637FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000337682ENST00000346144FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000337682ENST00000382683FAM60Achr12

31478960

-MADCAM1chr19

501667

+
intron-3CDSENST00000454658ENST00000587541FAM60Achr12

31478960

-MADCAM1chr19

501667

+
intron-3CDSENST00000454658ENST00000215637FAM60Achr12

31478960

-MADCAM1chr19

501667

+
intron-intronENST00000454658ENST00000346144FAM60Achr12

31478960

-MADCAM1chr19

501667

+
intron-intronENST00000454658ENST00000382683FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000395766ENST00000587541FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000395766ENST00000215637FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000395766ENST00000346144FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000395766ENST00000382683FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000542983ENST00000587541FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000542983ENST00000215637FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000542983ENST00000346144FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000542983ENST00000382683FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000536836ENST00000587541FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-3CDSENST00000536836ENST00000215637FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000536836ENST00000346144FAM60Achr12

31478960

-MADCAM1chr19

501667

+
5UTR-intronENST00000536836ENST00000382683FAM60Achr12

31478960

-MADCAM1chr19

501667

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for FAM60A-MADCAM1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
FAM60Achr1231478957-MADCAM1chr19501668+3.90E-091
FAM60Achr1231478957-MADCAM1chr19501668+3.90E-091
FAM60Achr1231478957-MADCAM1chr19501668+3.90E-091
FAM60Achr1231478957-MADCAM1chr19501668+3.90E-091

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for FAM60A-MADCAM1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
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.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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for FAM60A-MADCAM1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for FAM60A-MADCAM1


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for FAM60A-MADCAM1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for FAM60A-MADCAM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneMADCAM1C0009319Colitis1CTD_human
TgeneMADCAM1C0010093Corpus Luteum Cyst1CTD_human
TgeneMADCAM1C0029927Ovarian Cysts1CTD_human