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 NCOA1
Basic gene info.Gene symbolNCOA1
Gene namenuclear receptor coactivator 1
SynonymsF-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74
CytomapUCSC genome browser: 2p23
Genomic locationchr2 :24807345-24993570
Type of geneprotein-coding
RefGenesNM_003743.4,
NM_147223.2,NM_147233.2,
Ensembl idENSG00000084676
DescriptionHin-2 proteinPAX3/NCOA1 fusion proteinclass E basic helix-loop-helix protein 74renal carcinoma antigen NY-REN-52steroid receptor coactivator-1
Modification date20141207
dbXrefs MIM : 602691
HGNC : HGNC
Ensembl : ENSG00000084676
HPRD : 04070
Vega : OTTHUMG00000125523
ProteinUniProt: Q15788
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NCOA1
BioGPS: 8648
Gene Expression Atlas: ENSG00000084676
The Human Protein Atlas: ENSG00000084676
PathwayNCI Pathway Interaction Database: NCOA1
KEGG: NCOA1
REACTOME: NCOA1
ConsensusPathDB
Pathway Commons: NCOA1
MetabolismMetaCyc: NCOA1
HUMANCyc: NCOA1
RegulationEnsembl's Regulation: ENSG00000084676
miRBase: chr2 :24,807,345-24,993,570
TargetScan: NM_003743
cisRED: ENSG00000084676
ContextiHOP: NCOA1
cancer metabolism search in PubMed: NCOA1
UCL Cancer Institute: NCOA1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOA1 in cancer cell metabolism1. Qin L, Wu Y-L, Toneff MJ, Li D, Liao L, et al. (2014) NCOA1 Directly Targets M-CSF1 Expression to Promote Breast Cancer Metastasis. Cancer research 74: 3477-3488. go to article

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Phenotypic Information for NCOA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NCOA1
Familial Cancer Database: NCOA1
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602691; gene.
602691; gene.
Orphanet
DiseaseKEGG Disease: NCOA1
MedGen: NCOA1 (Human Medical Genetics with Condition)
ClinVar: NCOA1
PhenotypeMGI: NCOA1 (International Mouse Phenotyping Consortium)
PhenomicDB: NCOA1

Mutations for NCOA1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryNCOA1chr22483369424833714NCOA1chr22484733624847356
ovaryNCOA1chr22485363624853656NCOA1chr22485419624854216
ovaryNCOA1chr22492095524920975NCOA1chr22493595924935979
ovaryNCOA1chr22492336524923385ATAD2Bchr22413873524138755
ovaryNCOA1chr22497221224972232NCOA1chr22497228224972302
pancreasNCOA1chr22481372024813740chr28344786983447889
pancreasNCOA1chr22487117424871194NCOA1chr22487135724871377
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NCOA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW204594NCOA186422493050624930562NCOA16020122493030724930448
AY633656PAX319562223085940223163334NCOA1954286122494945624991385
AA319820NCOA11212422499280124992913NCOA112325622499288724993019
BX099622NCOA1110422499174124991843NOVA191309142706672127066939
BQ956364PCGF311654702588702753NCOA115771922493006424930624

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample             1   
GAIN (# sample)             1   
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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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=88)
Stat. for Synonymous SNVs
(# total SNVs=27)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr2:24929877-24929877p.S513L2
chr2:24962316-24962316p.R1073W2
chr2:24974859-24974859p.P1239S2
chr2:24985555-24985555p.?2
chr2:24928097-24928097p.I364I2
chr2:24929991-24929991p.S551F2
chr2:24916179-24916179p.T257T2
chr2:24949464-24949464p.P869H2
chr2:24929760-24929760p.S474Y1
chr2:24930637-24930637p.L766L1

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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
# sample621201 8 32 15113  1215115
# mutation821221 8 32 15123  1418122
nonsynonymous SNV821151 4 3  1172  713 19
synonymous SNV   7  4  2 451  7513
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
chr2:24985567p.P1239S,NCOA12
chr2:24974859p.P1359P,NCOA12
chr2:24930610p.E587D,NCOA11
chr2:24964741p.L766M,NCOA11
chr2:24896255p.S22L,NCOA11
chr2:24929492p.Q912Q,NCOA11
chr2:24933969p.E108Q,NCOA11
chr2:24981004p.G1162S,NCOA11
chr2:24916135p.G321D,NCOA11
chr2:24929854p.L1409L,NCOA11

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 NCOA1 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 NCOA1

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

ASXL2,ATF7,BAZ2B,BIRC6,BMPR2,CREB1,DNAJC27,
EXOC6B,GCC2,HEATR5B,ITSN2,KIDINS220,MAP3K2,NCOA1,
PUM2,RFX7,RGPD3,RGPD4,UBR3,USP34,ZNF510
ARHGEF12,ASH1L,ATG2B,ERCC6L2,AGO4,ICE1,KIAA1109,
KIAA2026,KMT2E,MYO9A,NCOA1,PIAS1,RANBP2,RGPD3,
SEC24B,SON,STAG1,TAB2,XRN1,ZBTB38,ZFX

BBX,BMPR2,CLASP1,CRIM1,CRYBG3,FRY,IL6ST,
INPP4A,IQSEC1,ITSN2,KIDINS220,NCOA1,PLSCR4,SEC14L1,
SETBP1,SIK3,SNRK,SOS1,SYNE1,USP34,WDFY3
AFF1,ARID1B,ASH1L,CAMTA2,CASZ1,DIDO1,FAM168B,
FXR2,GIGYF2,ZSWIM8,KIF13A,MED13L,MIA3,NCOA1,
NCOR2,NR2C2,RERE,SEC31A,SETD2,SUPT6H,USP34
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 NCOA1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q15788; -.
ChemistryChEMBL CHEMBL2095162; -.
ChemistryBindingDB Q15788; -.
ChemistryChEMBL CHEMBL2095162; -.
Organism-specific databasesPharmGKB PA31470; -.
Organism-specific databasesPharmGKB PA31470; -.
Organism-specific databasesCTD 8648; -.
Organism-specific databasesCTD 8648; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01645nuclear receptor coactivator 1experimentalGenistein
DB04652nuclear receptor coactivator 1experimental(11-BETA)-11,21-DIHYDROXY-PREGN-4-ENE-3,20-DIONE
DB06832nuclear receptor coactivator 1experimental2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL
DB06875nuclear receptor coactivator 1experimental3-(3-FLUORO-4-HYDROXYPHENYL)-7-HYDROXY-1-NAPHTHONITRILE
DB06908nuclear receptor coactivator 1experimental(2S)-3-(1-{[2-(2-CHLOROPHENYL)-5-METHYL-1,3-OXAZOL-4-YL]METHYL}-1H-INDOL-5-YL)-2-ETHOXYPROPANOIC ACID
DB06927nuclear receptor coactivator 1experimental[5-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-YL]ACETONITRILE
DB07009nuclear receptor coactivator 1experimental2-(5-HYDROXY-NAPHTHALEN-1-YL)-1,3-BENZOOXAZOL-6-OL
DB07080nuclear receptor coactivator 1experimentalN-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE
DB07119nuclear receptor coactivator 1experimental1-CHLORO-6-(4-HYDROXYPHENYL)-2-NAPHTHOL
DB07150nuclear receptor coactivator 1experimental4-(4-HYDROXYPHENYL)-1-NAPHTHALDEHYDE OXIME
DB07198nuclear receptor coactivator 1experimental5-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-CARBONITRILE
DB07215nuclear receptor coactivator 1experimental2-METHYL-2-(4-{[({4-METHYL-2-[4-(TRIFLUOROMETHYL)PHENYL]-1,3-THIAZOL-5-YL}CARBONYL)AMINO]METHYL}PHENOXY)PROPANOIC ACID
DB07230nuclear receptor coactivator 1experimental3-BROMO-6-HYDROXY-2-(4-HYDROXYPHENYL)-1H-INDEN-1-ONE
DB07236nuclear receptor coactivator 1experimental3-(6-HYDROXY-NAPHTHALEN-2-YL)-BENZO[D]ISOOXAZOL-6-OL
DB07530nuclear receptor coactivator 1experimental(1R,3R)-5-[(2E)-3-{(1S,3R)-2,2,3-trimethyl-3-[6,6,6-trifluoro-5-hydroxy-5-(trifluoromethyl)hex-3-yn-1-yl]cyclopentyl}prop-2-en-1-ylidene]cyclohexane-1,3-diol
DB07557nuclear receptor coactivator 1experimental(5BETA)-PREGNANE-3,20-DIONE
DB07724nuclear receptor coactivator 1experimental3-{5-methoxy-1-[(4-methoxyphenyl)sulfonyl]-1H-indol-3-yl}propanoic acid
DB08220nuclear receptor coactivator 1experimental(8alpha,10alpha,13alpha,17beta)-17-[(4-hydroxyphenyl)carbonyl]androsta-3,5-diene-3-carboxylic acid
DB08231nuclear receptor coactivator 1experimentalMYRISTIC ACID
DB08483nuclear receptor coactivator 1experimental(2S)-2-methoxy-3-{4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-1-benzothiophen-7-yl}propanoic acid
DB08742nuclear receptor coactivator 1experimental1,3-CYCLOHEXANEDIOL, 4-METHYLENE-5-[(2E)-[(1S,3AS,7AS)-OCTAHYDRO-1-(5-HYDROXY-5-METHYL-1,3-HEXADIYNYL)-7A-METHYL-4H-INDEN-4-YLIDENE]ETHYLIDENE]-, (1R,3S,5Z)
DB00755nuclear receptor coactivator 1approved; nutraceutical; investigationalTretinoin


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Cross referenced IDs for NCOA1
* 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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