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 CGA

Basic gene info.	Gene symbol	CGA
	Gene name	glycoprotein hormones, alpha polypeptide
	Synonyms	CG-ALPHA\|FSHA\|GPHA1\|GPHa\|HCG\|LHA\|TSHA
	Cytomap	UCSC genome browser: 6q12-q21
	Genomic location	chr6 :87795215-87804865
	Type of gene	protein-coding
	RefGenes	NM_000735.3, NM_001252383.1,
	Ensembl id	ENSG00000135346
	Description	FSH-alphaLSH-alphaTSH-alphaanterior pituitary glycoprotein hormones common subunit alphachoriogonadotropin alpha chainchorionic gonadotrophin subunit alphachorionic gonadotropin, alpha polypeptidefollicle-stimulating hormone alpha chainfollicle-st
	Modification date	20141207
dbXrefs	MIM : 118850
	HGNC : HGNC
	Ensembl : ENSG00000135346
	HPRD : 00342
	Vega : OTTHUMG00000015161
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CGA
	BioGPS: 1081
	Gene Expression Atlas: ENSG00000135346
	The Human Protein Atlas: ENSG00000135346
Pathway	NCI Pathway Interaction Database: CGA
	KEGG: CGA
	REACTOME: CGA
	ConsensusPathDB
	Pathway Commons: CGA
Metabolism	MetaCyc: CGA
	HUMANCyc: CGA
Regulation	Ensembl's Regulation: ENSG00000135346
	miRBase: chr6 :87,795,215-87,804,865
	TargetScan: NM_000735
	cisRED: ENSG00000135346
Context	iHOP: CGA
	cancer metabolism search in PubMed: CGA
	UCL Cancer Institute: CGA
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: CGA
	Familial Cancer Database: CGA

* 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_STEROID_HORMONES_AND_VITAMINS_A_AND_D REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: CGA
	MedGen: CGA (Human Medical Genetics with Condition)
	ClinVar: CGA
Phenotype	MGI: CGA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CGA

Mutations for CGA

* 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 CGA related fusion information.

ID	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
R81128	CGA	4	60	6	87795409	87795465	KDM5A	60	200	12	390470	390610
AV747863	SF1	1	281	11	64536509	64536969	CGA	278	530	6	87795966	87797907
CF528409	CGA	20	75	6	87795218	87795273	ZNF397	71	304	18	32823125	32825326
R02040	CGA	8	110	6	87795224	87795326	CDC42BPB	104	269	14	103488300	103488463
BQ367091	SMAD6	20	92	15	67040351	67040422	CGA	87	184	6	87795378	87795475
BF985831	CGA	17	290	6	87795224	87795497	PSMC2	283	415	7	103008430	103008562
R14891	CGA	1	111	6	87795216	87795326	CDC42BPB	105	362	14	103488300	103488549
AA368821	CGA	1	97	6	87795224	87795320	PRG2	87	155	11	57156671	57156739
BE842422	CASP10	11	149	2	202061083	202061223	CGA	142	363	6	87796110	87804814
AA441787	CGA	1	82	6	87795227	87795308	CGA	78	513	6	87795481	87804819
BQ012719	GUK1	18	120	1	228336550	228336652	CGA	115	444	6	87795223	87795552
AF370393	CGA	74	128	6	87795460	87795514	MFSD2A	129	1770	1	40432474	40435628
CF529503	GUK1	18	120	1	228336550	228336652	CGA	115	444	6	87795223	87795552
C19023	CGA	45	116	6	87795221	87795292	RAB1A	116	230	2	65357061	65357175

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=17)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr6:87796012-87796012	p.V77I	3
chr6:87796149-87796149	p.C31Y	2
chr6:87797846-87797846	p.A25S	2
chr6:87796037-87796037	p.K68K	1
chr6:87797874-87797874	p.L15L	1
chr6:87795511-87795511	p.A105V	1
chr6:87796049-87796049	p.P64P	1
chr6:87797884-87797884	p.L12P	1
chr6:87795514-87795514	p.T104M	1
chr6:87796062-87796062	p.A60E	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=2

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		1	1	3	1		1					6	2	1			2			2
# mutation		1	1	3	1		1					6	2	1			2			2
nonsynonymous SNV			1	3	1		1					2	2	1			2			1
synonymous SNV		1										4								1

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
chr6:87796149	p.V77I,CGA	2
chr6:87796012	p.C31Y,CGA	2
chr6:87795485	p.H114D,CGA	2
chr6:87796136	p.G96A,CGA	1
chr6:87795511	p.K75T,CGA	1
chr6:87795538	p.T70T,CGA	1
chr6:87797874	p.K68N,CGA	1
chr6:87797884	p.P64P,CGA	1
chr6:87796017	p.F57L,CGA	1
chr6:87796031	p.P45P,CGA	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 CGA 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 CGA

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


ADAM23,AVPI1,LINC00473,CCND2,CGA,CHRND,CYP2C18, ECEL1,ERMN,FAAH2,FAM13A,GDF10,LOC441177,MCF2, PCDHGB3,PTP4A1,RASL10B,RNF182,TAPBPL,UPK3BL,ZNF488	C14orf177,CALCA,CGA,CLEC3A,COL10A1,CST1,EGR4, GATA4,IL20,INSL4,KIR3DP1,LCE1D,LOC146336,MMP11, LINC00052,SCARNA20,SLC24A2,SLC30A8,SNORA80E,TPO,TYR

BTBD17,CGA,CSH1,DEFB107A,FAM197Y2,FAM27L,FEV, FLJ36000,KRTAP20-4,LCE1A,LOC642929,NCAN,NEUROD2,OR2L8, OR5H2,RBMY1A3P,SCGB1D4,SELV,SLC6A5,TFAP2B,TFAP2D, TSPY1,TSPY4,ZN	CGA,CSAG1,HYPM,FAM177B,STRIP2,GABRG3,IGF2BP3, KLK6,LOC100133893,OR2T5,PABPN1L,POU3F1,PPY,SEMG1, SFTA2,SLC39A7,SYTL5,T,TCL1B,TRH,WDR66

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 CGA

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB02944	glycoprotein hormones, alpha polypeptide	experimental	Alpha-D-Mannose
DB00451	glycoprotein hormones, alpha polypeptide	approved	Levothyroxine

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Cross referenced IDs for CGA

* 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