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 INHA

Basic gene info.	Gene symbol	INHA
	Gene name	inhibin, alpha
	Synonyms	-
	Cytomap	UCSC genome browser: 2q35
	Genomic location	chr2 :220436953-220440435
	Type of gene	protein-coding
	RefGenes	NM_002191.3,
	Ensembl id	ENSG00000123999
	Description	A-inhibin subunitinhibin alpha chain
	Modification date	20141219
dbXrefs	MIM : 147380
	HGNC : HGNC
	Ensembl : ENSG00000123999
	HPRD : 00933
	Vega : OTTHUMG00000059237
Protein	UniProt: P05111 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_INHA
	BioGPS: 3623
	Gene Expression Atlas: ENSG00000123999
	The Human Protein Atlas: ENSG00000123999
Pathway	NCI Pathway Interaction Database: INHA
	KEGG: INHA
	REACTOME: INHA
	ConsensusPathDB
	Pathway Commons: INHA
Metabolism	MetaCyc: INHA
	HUMANCyc: INHA
Regulation	Ensembl's Regulation: ENSG00000123999
	miRBase: chr2 :220,436,953-220,440,435
	TargetScan: NM_002191
	cisRED: ENSG00000123999
Context	iHOP: INHA
	cancer metabolism search in PubMed: INHA
	UCL Cancer Institute: INHA
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: INHA
	Familial Cancer Database: INHA

* 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	147380; gene.
Orphanet
Disease	KEGG Disease: INHA
	MedGen: INHA (Human Medical Genetics with Condition)
	ClinVar: INHA
Phenotype	MGI: INHA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: INHA

Mutations for INHA

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows INHA 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

There's no copy number variation information in COSMIC data for this gene.

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=24)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr2:220439659-220439659	p.H171R	3
chr2:220440019-220440019	p.C291S	2
chr2:220439886-220439886	p.R247C	2
chr2:220439678-220439678	p.A177A	2
chr2:220439723-220439723	p.P192P	2
chr2:220439824-220439824	p.G226E	1
chr2:220437270-220437270	p.L58L	1
chr2:220439993-220439993	p.Y282Y	1
chr2:220439618-220439618	p.L157L	1
chr2:220440183-220440183	p.G346R	1

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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=3

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	3	1		8			3					2	3	1			8	3		3
# mutation	3	1		8			3					2	3	1			8	3		3
nonsynonymous SNV	1	1		5			1					1	3	1			3	3		1
synonymous SNV	2			3			2					1					5			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
chr2:220440019	p.C291Y	2
chr2:220439993	p.R61I	1
chr2:220437228	p.G275C	1
chr2:220439822	p.L102L	1
chr2:220440018	p.R278L	1
chr2:220437229	p.P117P	1
chr2:220439824	p.W279C	1
chr2:220437278	p.G136G	1
chr2:220439842	p.Y282Y	1
chr2:220440061	p.A144D	1

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 INHA 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 INHA

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


AADAC,C1orf141,FOXL2NB,MGARP,CELA2A,CYP11A1,CYP17A1, CYP19A1,FSHR,GRAMD1B,HSD3B1,INHA,INSL3,KLHL4, LHCGR,MBOAT4,MRO,REG3G,STAR,TCF21,TREML5P	ARHGAP33,DDX39B,CYP2E1,DCST2,DOC2A,FAM193B,FER1L4, IFT27,INHA,JMJD7-PLA2G4B,KAT2A,L3MBTL1,LOC284900,LOC338799, MAPK15,MST1,NTN5,OVGP1,PABPC1L,SLC26A10,STRC

AKAP12,AP3B2,LINC00323,CACNA2D4,CHRNB2,CLVS1,HOXC13, INHA,KCNH4,MAPK8IP2,OBSL1,PRKCG,RAB3C,RGS7, RTBDN,SIRT1,SLC4A3,STX1A,TMEM198,TXNDC2,WNT10B	ANGPTL2,ARL10,C1orf95,CHRM3,COL6A1,COL6A3,FADS1, HHIPL1,HIST2H2BA,INHA,KCND3,KCNQ4,KIRREL,LAMA5, MID1IP1,NCKAP5L,NFIC,NLGN2,PTPN14,PXDN,RYR2

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 INHA

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA29876; -.
Organism-specific databases	CTD	3623; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00609	inhibin, alpha	approved	Ethionamide
DB00951	inhibin, alpha	approved	Isoniazid
DB01907	inhibin, alpha	experimental	Nicotinamide-Adenine-Dinucleotide
DB02990	inhibin, alpha	experimental	C16-Fatty-Acyl-Substrate-Mimic
DB04289	inhibin, alpha	experimental	Genz-10850
DB07090	inhibin, alpha	experimental	(3S)-N-(3-CHLORO-2-METHYLPHENYL)-1-CYCLOHEXYL-5-OXOPYRROLIDINE-3-CARBOXAMIDE
DB07123	inhibin, alpha	experimental	N-(4-METHYLBENZOYL)-4-BENZYLPIPERIDINE
DB07155	inhibin, alpha	experimental	(3S)-1-CYCLOHEXYL-5-OXO-N-PHENYLPYRROLIDINE-3-CARBOXAMIDE
DB07178	inhibin, alpha	experimental	5-PENTYL-2-PHENOXYPHENOL
DB07188	inhibin, alpha	experimental	(3S)-1-CYCLOHEXYL-N-(3,5-DICHLOROPHENYL)-5-OXOPYRROLIDINE-3-CARBOXAMIDE
DB07192	inhibin, alpha	experimental	(3S)-N-(3-BROMOPHENYL)-1-CYCLOHEXYL-5-OXOPYRROLIDINE-3-CARBOXAMIDE
DB07222	inhibin, alpha	experimental	(3S)-N-(5-CHLORO-2-METHYLPHENYL)-1-CYCLOHEXYL-5-OXOPYRROLIDINE-3-CARBOXAMIDE
DB07287	inhibin, alpha	experimental	2-(2,4-DICHLOROPHENOXY)-5-(PYRIDIN-2-YLMETHYL)PHENOL
DB08604	inhibin, alpha	experimental	TRICLOSAN
DB04393	inhibin, alpha	experimental	Diclosan
DB01691	inhibin, alpha	experimental	Indole Naphthyridinone
DB01865	inhibin, alpha	experimental	3-(6-Aminopyridin-3-Yl)-N-Methyl-N-[(1-Methyl-1h-Indol-2-Yl)Methyl]Acrylamide
DB02379	inhibin, alpha	experimental	Beta-D-Glucose
DB03030	inhibin, alpha	experimental	4-(2-Thienyl)-1-(4-Methylbenzyl)-1h-Imidazole
DB03534	inhibin, alpha	experimental	3-[(Acetyl-Methyl-Amino)-Methyl]-4-Amino-N-Methyl-N-(1-Methyl-1h-Indol-2-Ylmethyl)-Benzamide
DB04030	inhibin, alpha	experimental	1,3,4,9-Tetrahydro-2-(Hydroxybenzoyl)-9-[(4-Hydroxyphenyl)Methyl]-6-Methoxy-2h-Pyrido[3,4-B]Indole
DB08265	inhibin, alpha	experimental	2-(TOLUENE-4-SULFONYL)-2H-BENZO[D][1,2,3]DIAZABORININ-1-OL
DB08605	inhibin, alpha	experimental	6-METHYL-2(PROPANE-1-SULFONYL)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-OL

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Cross referenced IDs for INHA

* 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