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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
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 | Significant driver gene in |
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) |
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 |
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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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=17) | (# total SNVs=7) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr6:87796031-87796031 | p.T70T | 1 |
chr6:87797872-87797872 | p.S16L | 1 |
chr6:87795510-87795510 | p.A105A | 1 |
chr6:87796037-87796037 | p.K68K | 1 |
chr6:87797874-87797874 | p.L15L | 1 |
chr6:87795511-87795511 | p.A105V | 1 |
chr6:87796049-87796049 | p.P64P | 1 |
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SNV Counts per Each Loci in TCGA data |
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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.C31Y,CGA | 2 |
chr6:87796012 | p.H114D,CGA | 2 |
chr6:87795485 | p.V77I,CGA | 2 |
chr6:87796111 | p.L15L,CGA | 1 |
chr6:87795510 | p.L12P,CGA | 1 |
chr6:87796136 | p.Y113F,CGA | 1 |
chr6:87795511 | p.A105A,CGA | 1 |
chr6:87795538 | p.A105V,CGA | 1 |
chr6:87797874 | p.G96A,CGA | 1 |
chr6:87797884 | p.K75T,CGA | 1 |
Other DBs for Point Mutations |
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. |
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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 |
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 |
* 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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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