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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:ATOH8-GNLY (FusionGDB2 ID:7681)

Fusion Gene Summary for ATOH8-GNLY

check button Fusion gene summary
Fusion gene informationFusion gene name: ATOH8-GNLY
Fusion gene ID: 7681
HgeneTgene
Gene symbol

ATOH8

GNLY

Gene ID

84913

10578

Gene nameatonal bHLH transcription factor 8granulysin
SynonymsHATH6|bHLHa21D2S69E|LAG-2|LAG2|NKG5|TLA519
Cytomap

2p11.2

2p11.2

Type of geneprotein-codingprotein-coding
Descriptionprotein atonal homolog 8atonal homolog 6atonal homolog 8atonal homolog bHLH transcription factor 8basic helix loop helix transcription factor 6class A basic helix-loop-helix protein 21helix-loop-helix protein hATH-6granulysinT-cell activation protein 519T-lymphocyte activation gene 519lymphocyte-activation gene 2lymphokine LAG-2
Modification date2020031320200313
UniProtAcc

Q96SQ7

P22749

Ensembl transtripts involved in fusion geneENST00000463422, ENST00000306279, 
ENST00000263863, ENST00000524600, 
ENST00000409696, ENST00000533041, 
Fusion gene scores* DoF score4 X 2 X 3=244 X 3 X 4=48
# samples 56
** MAII scorelog2(5/24*10)=1.05889368905357
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(6/48*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ATOH8 [Title/Abstract] AND GNLY [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATOH8(85991305)-GNLY(85922443), # samples:3
ATOH8(85982080)-GNLY(85922443), # samples:3
Anticipated loss of major functional domain due to fusion event.ATOH8-GNLY seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ATOH8-GNLY seems lost the major protein functional domain in Hgene partner, which is a transcription factor 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
HgeneATOH8

GO:0045603

positive regulation of endothelial cell differentiation

24463812

HgeneATOH8

GO:0045893

positive regulation of transcription, DNA-templated

24236640

HgeneATOH8

GO:0060395

SMAD protein signal transduction

24236640

TgeneGNLY

GO:0006968

cellular defense response

9756476

TgeneGNLY

GO:0031640

killing of cells of other organism

9756476

TgeneGNLY

GO:0042742

defense response to bacterium

9756476

TgeneGNLY

GO:0061844

antimicrobial humoral immune response mediated by antimicrobial peptide

9756476


check buttonFusion gene breakpoints across ATOH8 (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 GNLY (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
ChimerDB4LUADTCGA-69-7978-01AATOH8chr2

85991305

-GNLYchr2

85922443

+
ChimerDB4LUADTCGA-69-7978-01AATOH8chr2

85991305

+GNLYchr2

85922443

+
ChimerDB4LUADTCGA-86-8673-01AATOH8chr2

85982080

-GNLYchr2

85922443

+
ChimerDB4LUADTCGA-86-8673-01AATOH8chr2

85982080

+GNLYchr2

85922443

+


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Fusion Gene ORF analysis for ATOH8-GNLY

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
3UTR-3CDSENST00000463422ENST00000263863ATOH8chr2

85991305

+GNLYchr2

85922443

+
3UTR-3CDSENST00000463422ENST00000263863ATOH8chr2

85982080

+GNLYchr2

85922443

+
3UTR-3CDSENST00000463422ENST00000524600ATOH8chr2

85991305

+GNLYchr2

85922443

+
3UTR-3CDSENST00000463422ENST00000524600ATOH8chr2

85982080

+GNLYchr2

85922443

+
3UTR-3UTRENST00000463422ENST00000409696ATOH8chr2

85991305

+GNLYchr2

85922443

+
3UTR-3UTRENST00000463422ENST00000409696ATOH8chr2

85982080

+GNLYchr2

85922443

+
3UTR-3UTRENST00000463422ENST00000533041ATOH8chr2

85991305

+GNLYchr2

85922443

+
3UTR-3UTRENST00000463422ENST00000533041ATOH8chr2

85982080

+GNLYchr2

85922443

+
5CDS-3UTRENST00000306279ENST00000409696ATOH8chr2

85991305

+GNLYchr2

85922443

+
5CDS-3UTRENST00000306279ENST00000409696ATOH8chr2

85982080

+GNLYchr2

85922443

+
5CDS-3UTRENST00000306279ENST00000533041ATOH8chr2

85991305

+GNLYchr2

85922443

+
5CDS-3UTRENST00000306279ENST00000533041ATOH8chr2

85982080

+GNLYchr2

85922443

+
Frame-shiftENST00000306279ENST00000263863ATOH8chr2

85991305

+GNLYchr2

85922443

+
Frame-shiftENST00000306279ENST00000263863ATOH8chr2

85982080

+GNLYchr2

85922443

+
Frame-shiftENST00000306279ENST00000524600ATOH8chr2

85991305

+GNLYchr2

85922443

+
Frame-shiftENST00000306279ENST00000524600ATOH8chr2

85982080

+GNLYchr2

85922443

+

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 ATOH8-GNLY


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)
ATOH8chr285982080+GNLYchr285922442+0.03022160.96977836
ATOH8chr285991305+GNLYchr285922442+9.93E-050.9999007
ATOH8chr285982080+GNLYchr285922442+0.03022160.96977836
ATOH8chr285991305+GNLYchr285922442+9.93E-050.9999007

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.
genomic feature of top 1%

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Fusion Protein Features for ATOH8-GNLY


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/:85991305/:85922443)
- 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
ATOH8

Q96SQ7

GNLY

P22749

FUNCTION: Transcription factor that binds a palindromic (canonical) core consensus DNA sequence 5'-CANNTG- 3' known as an E-box element, possibly as a heterodimer with other bHLH proteins (PubMed:24236640). Regulates endothelial cell proliferation, migration and tube-like structures formation (PubMed:24463812). Modulates endothelial cell differentiation through NOS3 (PubMed:24463812). May be implicated in specification and differentiation of neuronal cell lineages in the brain (By similarity). May participate in kidney development and may be involved in podocyte differentiation (By similarity). During early embryonic development is involved in tissue-specific differentiation processes that are dependent on class II bHLH factors and namely modulates the differentiation program initiated by the pro-endocrine factor NEUROG3 (By similarity). During myogenesis, may play a role during the transition of myoblasts from the proliferative phase to the differentiation phase (By similarity). Positively regulates HAMP transcription in two ways, firstly by acting directly on the HAMP promoter via E-boxes binding and indirectly through increased phosphorylation of SMAD protein complex (PubMed:24236640). Repress NEUROG3-dependent gene activation in a gene-specific manner through at least two mechanisms; requires only either the sequestering of a general partner such as TCF3 through heterodimerization, either also requires binding of the bHLH domain to DNA via a basic motif (By similarity). {ECO:0000250|UniProtKB:Q99NA2, ECO:0000269|PubMed:24236640, ECO:0000269|PubMed:24463812}.FUNCTION: Antimicrobial protein that kills intracellular pathogens. Active against a broad range of microbes, including Gram-positive and Gram-negative bacteria, fungi, and parasites. Kills Mycobacterium tuberculosis.

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 ATOH8-GNLY


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 ATOH8-GNLY


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 ATOH8-GNLY


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 ATOH8-GNLY


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