Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolCGA
Gene nameglycoprotein hormones, alpha polypeptide
SynonymsCG-ALPHA|FSHA|GPHA1|GPHa|HCG|LHA|TSHA
CytomapUCSC genome browser: 6q12-q21
Genomic locationchr6 :87795215-87804865
Type of geneprotein-coding
RefGenesNM_000735.3,
NM_001252383.1,
Ensembl idENSG00000135346
DescriptionFSH-alphaLSH-alphaTSH-alphaanterior pituitary glycoprotein hormones common subunit alphachoriogonadotropin alpha chainchorionic gonadotrophin subunit alphachorionic gonadotropin, alpha polypeptidefollicle-stimulating hormone alpha chainfollicle-st
Modification date20141207
dbXrefs MIM : 118850
HGNC : HGNC
Ensembl : ENSG00000135346
HPRD : 00342
Vega : OTTHUMG00000015161
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CGA
BioGPS: 1081
Gene Expression Atlas: ENSG00000135346
The Human Protein Atlas: ENSG00000135346
PathwayNCI Pathway Interaction Database: CGA
KEGG: CGA
REACTOME: CGA
ConsensusPathDB
Pathway Commons: CGA
MetabolismMetaCyc: CGA
HUMANCyc: CGA
RegulationEnsembl's Regulation: ENSG00000135346
miRBase: chr6 :87,795,215-87,804,865
TargetScan: NM_000735
cisRED: ENSG00000135346
ContextiHOP: CGA
cancer metabolism search in PubMed: CGA
UCL Cancer Institute: CGA
Assigned class in ccmGDBC

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Phenotypic Information for CGA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CGA
MedGen: CGA (Human Medical Genetics with Condition)
ClinVar: CGA
PhenotypeMGI: CGA (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CGA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
R81128CGA46068779540987795465KDM5A6020012390470390610
AV747863SF11281116453650964536969CGA27853068779596687797907
CF528409CGA207568779521887795273ZNF39771304183282312532825326
R02040CGA811068779522487795326CDC42BPB10426914103488300103488463
BQ367091SMAD62092156704035167040422CGA8718468779537887795475
BF985831CGA1729068779522487795497PSMC22834157103008430103008562
R14891CGA111168779521687795326CDC42BPB10536214103488300103488549
AA368821CGA19768779522487795320PRG287155115715667157156739
BE842422CASP10111492202061083202061223CGA14236368779611087804814
AA441787CGA18268779522787795308CGA7851368779548187804819
BQ012719GUK1181201228336550228336652CGA11544468779522387795552
AF370393CGA7412868779546087795514MFSD2A129177014043247440435628
CF529503GUK1181201228336550228336652CGA11544468779522387795552
C19023CGA4511668779522187795292RAB1A11623026535706165357175

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr6:87796012-87796012p.V77I3
chr6:87796149-87796149p.C31Y2
chr6:87797846-87797846p.A25S2
chr6:87795510-87795510p.A105A1
chr6:87796037-87796037p.K68K1
chr6:87797874-87797874p.L15L1
chr6:87795511-87795511p.A105V1
chr6:87796049-87796049p.P64P1
chr6:87797884-87797884p.L12P1
chr6:87795514-87795514p.T104M1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample 1131 1    621  2  2
# mutation 1131 1    621  2  2
nonsynonymous SNV  131 1    221  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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr6:87796149p.C31Y,CGA2
chr6:87796012p.H114D,CGA2
chr6:87795485p.V77I,CGA2
chr6:87795510p.T35T,CGA1
chr6:87796136p.L15L,CGA1
chr6:87795511p.L12P,CGA1
chr6:87795538p.Y113F,CGA1
chr6:87797874p.A105A,CGA1
chr6:87797884p.A105V,CGA1
chr6:87796017p.G96A,CGA1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02944glycoprotein hormones, alpha polypeptideexperimentalAlpha-D-Mannose
DB00451glycoprotein hormones, alpha polypeptideapprovedLevothyroxine


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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



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