Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for INHBA

Basic gene info.	Gene symbol	INHBA
	Gene name	inhibin, beta A
	Synonyms	EDF\|FRP
	Cytomap	UCSC genome browser: 7p15-p13
	Genomic location	chr7 :41728600-41742706
	Type of gene	protein-coding
	RefGenes	NM_002192.2,
	Ensembl id	ENSG00000122641
	Description	FSH-releasing proteinInhibin, beta-1activin beta-A chainerythroid differentiation factorerythroid differentiation proteinfollicle-stimulating hormone-releasing proteininhibin beta A chaininhibin, beta A (activin A, activin AB alpha polypeptide)
	Modification date	20141222
dbXrefs	MIM : 147290
	HGNC : HGNC
	HPRD : 00929
Protein	UniProt: P08476 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_INHBA
	BioGPS: 3624
	Gene Expression Atlas: ENSG00000122641
	The Human Protein Atlas: ENSG00000122641
Pathway	NCI Pathway Interaction Database: INHBA
	KEGG: INHBA
	REACTOME: INHBA
	ConsensusPathDB
	Pathway Commons: INHBA
Metabolism	MetaCyc: INHBA
	HUMANCyc: INHBA
Regulation	Ensembl's Regulation: ENSG00000122641
	miRBase: chr7 :41,728,600-41,742,706
	TargetScan: NM_002192
	cisRED: ENSG00000122641
Context	iHOP: INHBA
	cancer metabolism search in PubMed: INHBA
	UCL Cancer Institute: INHBA
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for INHBA(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: INHBA
	Familial Cancer Database: INHBA

* This gene is included in those cancer gene databases.


Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM	147290; gene.
Orphanet	213504; Adenocarcinoma of ovary.
Disease	KEGG Disease: INHBA
	MedGen: INHBA (Human Medical Genetics with Condition)
	ClinVar: INHBA
Phenotype	MGI: INHBA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: INHBA

Mutations for INHBA

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	INHBA	chr7	41735899	41735899		chr15	84072371	84072371
ovary	INHBA	chr7	41740856	41740876	INHBA	chr7	41736244	41736264

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows INHBA related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=96)	Stat. for Synonymous SNVs (# total SNVs=24)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=3)

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr7:41739626-41739626	p.L116P	3
chr7:41729708-41729708	p.G274V	3
chr7:41729709-41729709	p.G274R	3
chr7:41729399-41729399	p.R377H	3
chr7:41729272-41729272	p.I419I	3
chr7:41729749-41729749	p.K260K	2
chr7:41729601-41729601	p.R310W	2
chr7:41729504-41729504	p.P342L	2
chr7:41739731-41739731	p.A81V	2
chr7:41729388-41729388	p.H381fs*16	2

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	5		22	3		1		2			26	6	2		2	19	12	2	8
# mutation	2	5		20	3		1		2			26	6	2		2	22	11	2	9
nonsynonymous SNV		2		16	2		1		2			21	5	2		2	17	9	2	7
synonymous SNV	2	3		4	1							5	1				5	2		2

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr7:41729399	p.R377H	3
chr7:41729272	p.I419I	3
chr7:41739626	p.T217I	2
chr7:41729504	p.K215E	2
chr7:41739824	p.A81E	2
chr7:41729665	p.R310W	2
chr7:41729928	p.R379Q	2
chr7:41739857	p.A252T	2
chr7:41729393	p.E139D	2
chr7:41729775	p.R379W	2

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for INHBA in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for INHBA

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


ADAMTS12,ADAMTS2,ANTXR1,CDH11,COL10A1,COL11A1,COL12A1, COL5A2,COL8A1,DACT1,FAM26E,FAP,FBN1,FN1, INHBA,ITGA11,MXRA5,NID2,NOX4,THBS2,VCAN	A2ML1,ATP8B2,VRTN,C3orf30,CNTN4,SPATA31A2,HSD17B6, INHBA,ITGA8,ITIH3,KIF1A,LOC153910,MRVI1,P2RX1, RYR2,SCUBE3,SMAD9,SUSD5,TRPC4,WFDC1,ZFP42

ADAMTS12,ARSI,BICC1,CDK14,CERCAM,COL11A1,COL1A2, COL5A1,COL5A2,COL6A3,FRMD6,GPC6,INHBA,KCND2, PDGFC,PDGFRB,POSTN,SPARC,TIMP2,VASN,VCAN	ABL2,ADAMTS9,ALPL,AOC2,AVPR1A,CFAP46,C1orf111, AGO2,FAM98A,INHBA,LDLRAD3,LRP8,MAP3K6,NOV, NOVA2,OSMR,SELP,SH3RF3,SHISA6,SRM,VEGFC

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for INHBA

There's no related Drug.

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Cross referenced IDs for INHBA

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information