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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:ITGA5-MMP9 (FusionGDB2 ID:40436)

Fusion Gene Summary for ITGA5-MMP9

Fusion gene summary

Fusion gene information	Fusion gene name: ITGA5-MMP9
	Fusion gene ID: 40436
		Hgene	Tgene
	Gene symbol	ITGA5	MMP9
	Gene ID	3678	4318
	Gene name	integrin subunit alpha 5	matrix metallopeptidase 9
	Synonyms	CD49e\|FNRA\|VLA-5\|VLA5A	CLG4B\|GELB\|MANDP2\|MMP-9
	Cytomap	12q13.13	20q13.12
	Type of gene	protein-coding	protein-coding
	Description	integrin alpha-5CD49 antigen-like family member EITGA5/SLC9B1 fusionfibronectin receptor subunit alphafibronectin receptor, alpha polypeptidefibronectin receptor, alpha subunitintegrin alpha-Fintegrin, alpha 5 (fibronectin receptor, alpha polypepti	matrix metalloproteinase-9macrophage gelatinasematrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)type V collagenase
	Modification date	20200329	20200329
	UniProtAcc	P08648	P14780
	Ensembl transtripts involved in fusion gene	ENST00000293379, ENST00000547744,	ENST00000372330,
Fusion gene scores	* DoF score	3 X 4 X 4=48	5 X 4 X 4=80
	# samples	4	5
	** MAII score	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/80*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: ITGA5 [Title/Abstract] AND MMP9 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	ITGA5(54805618)-MMP9(44642763), # samples:1
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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	ITGA5	GO:0007155	cell adhesion	19703720
Hgene	ITGA5	GO:0007229	integrin-mediated signaling pathway	31331973
Hgene	ITGA5	GO:0023035	CD40 signaling pathway	31331973
Hgene	ITGA5	GO:0033627	cell adhesion mediated by integrin	12807887\|17158881
Tgene	MMP9	GO:0006508	proteolysis	2551898\|15863497\|19022250\|24164424
Tgene	MMP9	GO:0034614	cellular response to reactive oxygen species	26514923
Tgene	MMP9	GO:0043388	positive regulation of DNA binding	22984561
Tgene	MMP9	GO:0071276	cellular response to cadmium ion	26514923
Tgene	MMP9	GO:1900122	positive regulation of receptor binding	24164424
Tgene	MMP9	GO:2001258	negative regulation of cation channel activity	24164424

Fusion gene breakpoints across ITGA5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across MMP9 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	SARC	TCGA-HB-A2OT-01A	ITGA5	chr12	54805618	-	MMP9	chr20	44642763	+

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Fusion Gene ORF analysis for ITGA5-MMP9

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
In-frame	ENST00000293379	ENST00000372330	ITGA5	chr12	54805618	-	MMP9	chr20	44642763	+
intron-3CDS	ENST00000547744	ENST00000372330	ITGA5	chr12	54805618	-	MMP9	chr20	44642763	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

ENST00000293379

ITGA5

chr12

54805618

ENST00000372330

MMP9

chr20

44642763

1178

611

115

984

289

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000293379	ENST00000372330	ITGA5	chr12	54805618	-	MMP9	chr20	44642763	+	0.40632367	0.5936764

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Fusion Genomic Features for ITGA5-MMP9

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
ITGA5	chr12	54805617	-	MMP9	chr20	44642762	+	0.001308765	0.99869126
ITGA5	chr12	54805617	-	MMP9	chr20	44642762	+	0.001308765	0.99869126

Distribution 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.

Distribution 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 ITGA5-MMP9

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:54805618/chr20:44642763)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
ITGA5 P08648	MMP9 P14780
FUNCTION: Integrin alpha-5/beta-1 (ITGA5:ITGB1) is a receptor for fibronectin and fibrinogen. It recognizes the sequence R-G-D in its ligands. ITGA5:ITGB1 binds to PLA2G2A via a site (site 2) which is distinct from the classical ligand-binding site (site 1) and this induces integrin conformational changes and enhanced ligand binding to site 1 (PubMed:18635536, PubMed:25398877). ITGA5:ITGB1 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1 (PubMed:12807887, PubMed:17158881). ITGA5:ITGB1 is a receptor for IL1B and binding is essential for IL1B signaling (PubMed:29030430). ITGA5:ITGB3 is a receptor for soluble CD40LG and is required for CD40/CD40LG signaling (PubMed:31331973). {ECO:0000269\|PubMed:12807887, ECO:0000269\|PubMed:17158881, ECO:0000269\|PubMed:18635536, ECO:0000269\|PubMed:25398877, ECO:0000269\|PubMed:29030430, ECO:0000269\|PubMed:31331973}.; FUNCTION: (Microbial infection) Integrin ITGA5:ITGB1 acts as a receptor for Human metapneumovirus. {ECO:0000269\|PubMed:12907437}.; FUNCTION: (Microbial infection) Integrin ITGA2:ITGB1 acts as a receptor for Human parvovirus B19. {ECO:0000269\|PubMed:24478423}.; FUNCTION: (Microbial infection) In case of HIV-1 infection, the interaction with extracellular viral Tat protein seems to enhance angiogenesis in Kaposi's sarcoma lesions. {ECO:0000269\|PubMed:10397733}.	FUNCTION: May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-\|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide. {ECO:0000269\|PubMed:1480034}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

43_108

116

1050.0

Repeat

FG-GAP 1

Tgene

MMP9

chr12:54805618

chr20:44642763

ENST00000372330

610_657

583

708.0

Repeat

Note=Hemopexin 3

Tgene

MMP9

chr12:54805618

chr20:44642763

ENST00000372330

658_704

583

708.0

Repeat

Note=Hemopexin 4

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

280_288

116

1050.0

Calcium binding

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

334_342

116

1050.0

Calcium binding

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

401_409

116

1050.0

Calcium binding

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

465_473

116

1050.0

Calcium binding

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

1024_1028

116

1050.0

Motif

Note=GFFKR motif

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

128_188

116

1050.0

Repeat

FG-GAP 2

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

192_245

116

1050.0

Repeat

FG-GAP 3

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

259_311

116

1050.0

Repeat

FG-GAP 4

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

312_377

116

1050.0

Repeat

FG-GAP 5

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

378_437

116

1050.0

Repeat

FG-GAP 6

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

441_504

116

1050.0

Repeat

FG-GAP 7

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

1022_1049

116

1050.0

Topological domain

Cytoplasmic

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

42_995

116

1050.0

Topological domain

Extracellular

Hgene

ITGA5

chr12:54805618

chr20:44642763

ENST00000293379

996_1021

116

1050.0

Transmembrane

Helical

Tgene

MMP9

chr12:54805618

chr20:44642763

ENST00000372330

225_273

583

708.0

Domain

Fibronectin type-II 1

Tgene

MMP9

chr12:54805618

chr20:44642763

ENST00000372330

283_331

583

708.0

Domain

Fibronectin type-II 2

Tgene

MMP9

chr12:54805618

chr20:44642763

ENST00000372330

342_390

583

708.0

Domain

Fibronectin type-II 3

Tgene

MMP9

chr12:54805618

chr20:44642763

ENST00000372330

97_104

583

708.0

Motif

Cysteine switch

Tgene

MMP9

chr12:54805618

chr20:44642763

ENST00000372330

518_563

583

708.0

Repeat

Note=Hemopexin 1

Tgene

MMP9

chr12:54805618

chr20:44642763

ENST00000372330

564_608

583

708.0

Repeat

Note=Hemopexin 2

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Fusion Gene Sequence for ITGA5-MMP9

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.

>40436_40436_1_ITGA5-MMP9_ITGA5_chr12_54805618_ENST00000293379_MMP9_chr20_44642763_ENST00000372330_length(transcript)=1178nt_BP=611nt
AGTCCAGACAACCGGCTTCCAGCTGGGGCTGGGGAAAGGGGGTTGGAGGGGTGCGCCCCCCCCCCACGCCCCTTAGGGGTGGGGGACGCG
GGCTCAGAGTTCCAGGGACCCAGGAATGCCCCCCCGCCAGCCCCCTCGGCAGGCGGGGGGAGGGCTCAGCCGGGAGTTTGGCAAACTCCT
CCCCGCGTTGAGTCATTCGCCTCTGGGAGGTTTAGGAAGCGGCTCCGGGTCGGTGGCCCCAGGACAGGGAAGAGCGGGCGCTATGGGGAG
CCGGACGCCAGAGTCCCCTCTCCACGCCGTGCAGCTGCGCTGGGGCCCCCGGCGCCGACCCCCGCTGCTGCCGCTGCTGTTGCTGCTGCT
GCCGCCGCCACCCAGGGTCGGGGGCTTCAACTTAGACGCGGAGGCCCCAGCAGTACTCTCGGGGCCCCCGGGCTCCTTCTTCGGATTCTC
AGTGGAGTTTTACCGGCCGGGAACAGACGGGGTCAGTGTGCTGGTGGGAGCACCCAAGGCTAATACCAGCCAGCCAGGAGTGCTGCAGGG
TGGTGCTGTCTACCTCTGTCCTTGGGGTGCCAGCCCCACACAGTGCACCCCCATTGAATTTGACAGCAAAGGGCGCCAGGTGTGGGTGTA
CACAGGCGCGTCGGTGCTGGGCCCGAGGCGTCTGGACAAGCTGGGCCTGGGAGCCGACGTGGCCCAGGTGACCGGGGCCCTCCGGAGTGG
CAGGGGGAAGATGCTGCTGTTCAGCGGGCGGCGCCTCTGGAGGTTCGACGTGAAGGCGCAGATGGTGGATCCCCGGAGCGCCAGCGAGGT
GGACCGGATGTTCCCCGGGGTGCCTTTGGACACGCACGACGTCTTCCAGTACCGAGAGAAAGCCTATTTCTGCCAGGACCGCTTCTACTG
GCGCGTGAGTTCCCGGAGTGAGTTGAACCAGGTGGACCAAGTGGGCTACGTGACCTATGACATCCTGCAGTGCCCTGAGGACTAGGGCTC
CCGTCCTGCTTTGGCAGTGCCATGTAAATCCCCACTGGGACCAACCCTGGGGAAGGAGCCAGTTTGCCGGATACAAACTGGTATTCTGTT
CTGGAGGAAAGGGAGGAGTGGAGGTGGGCTGGGCCCTCTCTTCTCACCTTTGTTTTTTGTTGGAGTGTTTCTAATAAACTTGGATTCTCT

>40436_40436_1_ITGA5-MMP9_ITGA5_chr12_54805618_ENST00000293379_MMP9_chr20_44642763_ENST00000372330_length(amino acids)=289AA_BP=165
MPPRQPPRQAGGGLSREFGKLLPALSHSPLGGLGSGSGSVAPGQGRAGAMGSRTPESPLHAVQLRWGPRRRPPLLPLLLLLLPPPPRVGG
FNLDAEAPAVLSGPPGSFFGFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPWGASPTQCTPIEFDSKGRQVWVYTGASVLGP
RRLDKLGLGADVAQVTGALRSGRGKMLLFSGRRLWRFDVKAQMVDPRSASEVDRMFPGVPLDTHDVFQYREKAYFCQDRFYWRVSSRSEL

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

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Fusion Gene PPI Analysis for ITGA5-MMP9

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Hgene	ITGA5	chr12:54805618	chr20:44642763	ENST00000293379	-	2	30	1021_1028	116.33333333333333	1050.0	HPS5

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for ITGA5-MMP9

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for ITGA5-MMP9

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source