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 NCOA3
Basic gene info.Gene symbolNCOA3
Gene namenuclear receptor coactivator 3
SynonymsACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP
CytomapUCSC genome browser: 20q12
Genomic locationchr20 :46130600-46285621
Type of geneprotein-coding
RefGenesNM_001174087.1,
NM_001174088.1,NM_006534.3,NM_181659.2,
Ensembl idENSG00000124151
DescriptionCBP-interacting proteinamplified in breast cancer 1 proteinclass E basic helix-loop-helix protein 42receptor-associated coactivator 3steroid receptor coactivator protein 3thyroid hormone receptor activator molecule 1
Modification date20141207
dbXrefs MIM : 601937
HGNC : HGNC
Ensembl : ENSG00000124151
HPRD : 03570
Vega : OTTHUMG00000033061
ProteinUniProt: Q9Y6Q9
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NCOA3
BioGPS: 8202
Gene Expression Atlas: ENSG00000124151
The Human Protein Atlas: ENSG00000124151
PathwayNCI Pathway Interaction Database: NCOA3
KEGG: NCOA3
REACTOME: NCOA3
ConsensusPathDB
Pathway Commons: NCOA3
MetabolismMetaCyc: NCOA3
HUMANCyc: NCOA3
RegulationEnsembl's Regulation: ENSG00000124151
miRBase: chr20 :46,130,600-46,285,621
TargetScan: NM_001174087
cisRED: ENSG00000124151
ContextiHOP: NCOA3
cancer metabolism search in PubMed: NCOA3
UCL Cancer Institute: NCOA3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOA3 in cancer cell metabolism1. Wagner M, Koslowski M, Paret C, Schmidt M, Türeci Ö, et al. (2013) NCOA3 is a selective co-activator of estrogen receptor α-mediated transactivation of PLAC1 in MCF-7 breast cancer cells. BMC cancer 13: 570. go to article

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Phenotypic Information for NCOA3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NCOA3
Familial Cancer Database: NCOA3
* 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 601937; gene.
601937; gene.
Orphanet
DiseaseKEGG Disease: NCOA3
MedGen: NCOA3 (Human Medical Genetics with Condition)
ClinVar: NCOA3
PhenotypeMGI: NCOA3 (International Mouse Phenotyping Consortium)
PhenomicDB: NCOA3

Mutations for NCOA3
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryNCOA3chr204615874846158768chr223829421038294230
ovaryNCOA3chr204620647546206495NCOA3chr204620068446200704
ovaryNCOA3chr204625191846251938NCOA3chr204619782446197844
ovaryNCOA3chr204626185146261871SULF2chr204634070846340728
ovaryNCOA3chr204626185246261872SULF2chr204634070846340728
pancreasNCOA3chr204613872146138741chr204607845946078479
pancreasNCOA3chr204621396846213988chr157720814677208166
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 NCOA3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA523336NCOA31109204613065746130765SLAIN1106549137829366578318569
DB144841NCOA31107204613065746130763TXNDC5106547678998768002806
BQ009202C4orf4818285420441372045691NCOA3283698204627587646279816
BF839348ANTXR1923426935019869397409NCOA3229372204621917146219314
BP292769STAT5B1496174035957140362610NCOA3493552204626991346269972
DA853259NCOA34139204613062846130763ZMYND8138570204592060945938950
F12469NCOA31114204613289946133012CD3611215278012570780125747
BE832543XPO61112162815750628164073NCOA3112188204626542246265498
AI571643SPINK112335147204146147207693NCOA3225406204623266246232843

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 # sample4  2  1 4 5   2  
GAIN (# sample)4  2  1 4 5   2  
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=17

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=97)
Stat. for Synonymous SNVs
(# total SNVs=62)
Stat. for Deletions
(# total SNVs=26)
Stat. for Insertions
(# total SNVs=4)

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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
chr20:46279837-46279839p.Q1255delQ17
chr20:46279860-46279860p.Q1262Q12
chr20:46279830-46279830p.Q1252Q6
chr20:46279839-46279839p.Q1255Q6
chr20:46279827-46279827p.Q1251Q5
chr20:46279836-46279836p.Q1254Q5
chr20:46264449-46264449p.P499L4
chr20:46279834-46279836p.Q1254delQ4
chr20:46265284-46265284p.D718D3
chr20:46279866-46279866p.Q1264Q3

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample581202 6 41 1344  1517112
# mutation581212 6 41 1644  1518113
nonsynonymous SNV481151 4 41 1143  1212110
synonymous SNV1  61 2    5 1  36 3
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
chr20:46279860p.Q1261Q,NCOA33
chr20:46264449p.P499H,NCOA33
chr20:46281213p.F1279F,NCOA32
chr20:46255881p.A1303T,NCOA32
chr20:46281693p.P499P,NCOA32
chr20:46279914p.D165N,NCOA32
chr20:46279984p.S1336L,NCOA32
chr20:46265284p.D718D,NCOA32
chr20:46264450p.Q1379Q,NCOA32
chr20:46275921p.L804F,NCOA31

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 NCOA3 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 NCOA3

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

ADNP,ARFGEF1,ARFGEF2,C12orf66,CLOCK,CSE1L,DAAM1,
ELMO2,ITCH,MPHOSPH9,NCOA2,NCOA3,LTN1,SBNO1,
SERINC3,STAU1,STK4,TAF4,UBE2W,VPS13B,YWHAB
AHCTF1,ASXL2,BIRC6,CCNT1,CEP97,DENND4A,ELK4,
LATS1,MED13,KMT2C,KAT6A,NCOA3,LTN1,SETX,
SCAF11,SMCHD1,SMG1,STRN,VPS13B,VPS13C,XRN1

ADNP,ARFGEF2,ASXL1,ATP9A,SOGA1,CHD6,DIDO1,
ELMO2,ITCH,KIF3B,LOC647979,NCOA3,NCOA6,PHF20,
PPP1R3D,PTPN1,RALGAPB,RPRD1B,STAU1,STK4,TAF4
BEND4,DOCK8,ETS1,IKZF3,INPP5D,KCNC3,KDM5A,
KIAA0922,KLHL6,NCOA3,NUP210,P2RY8,PARP15,PAX5,
PLCG2,SNX29P2,SP140,STK4,TLR9,WDFY4,ZNF831
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 NCOA3


There's no related Drug.
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Cross referenced IDs for NCOA3
* 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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