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 NCOA6
Basic gene info.Gene symbolNCOA6
Gene namenuclear receptor coactivator 6
SynonymsAIB3|ASC2|NRC|PRIP|RAP250|TRBP
CytomapUCSC genome browser: 20q11
Genomic locationchr20 :33302577-33413433
Type of geneprotein-coding
RefGenesNM_001242539.1,
NM_014071.3,
Ensembl idENSG00000198646
DescriptionNRC RAP250PPAR-interacting proteinactivating signal cointegrator 2activating signal cointegrator-2amplified in breast cancer protein 3amplified in breast cancer-3 proteincancer-amplified transcriptional coactivator ASC-2nuclear receptor coactivator
Modification date20141207
dbXrefs MIM : 605299
HGNC : HGNC
Ensembl : ENSG00000198646
HPRD : 05599
Vega : OTTHUMG00000032311
ProteinUniProt: Q14686
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NCOA6
BioGPS: 23054
Gene Expression Atlas: ENSG00000198646
The Human Protein Atlas: ENSG00000198646
PathwayNCI Pathway Interaction Database: NCOA6
KEGG: NCOA6
REACTOME: NCOA6
ConsensusPathDB
Pathway Commons: NCOA6
MetabolismMetaCyc: NCOA6
HUMANCyc: NCOA6
RegulationEnsembl's Regulation: ENSG00000198646
miRBase: chr20 :33,302,577-33,413,433
TargetScan: NM_001242539
cisRED: ENSG00000198646
ContextiHOP: NCOA6
cancer metabolism search in PubMed: NCOA6
UCL Cancer Institute: NCOA6
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOA6 in cancer cell metabolism1. Srihari S, Ragan MA (2013) Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics: btt191. go to article

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Phenotypic Information for NCOA6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NCOA6
Familial Cancer Database: NCOA6
* 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 605299; gene.
Orphanet
DiseaseKEGG Disease: NCOA6
MedGen: NCOA6 (Human Medical Genetics with Condition)
ClinVar: NCOA6
PhenotypeMGI: NCOA6 (International Mouse Phenotyping Consortium)
PhenomicDB: NCOA6

Mutations for NCOA6
* 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
ovaryNCOA6chr203333201133332031chr69060183390601853
ovaryNCOA6chr203339786833397888NCOA6chr203339846333398483
pancreasNCOA6chr203331427933314299CTCFLchr205609278656092806
pancreasNCOA6chr203331999933320019CTCFLchr205608893156088951
pancreasNCOA6chr203336115833361178ACSS2chr203351216033512180
pancreasNCOA6chr203337506133375081IFT52chr204226615542266175
pancreasNCOA6chr203338125133381271chr205610179356101813
pancreasNCOA6chr203339351933393539MIR5095chr205592647255926492
pancreasNCOA6chr203340243633402456PKIGchr204316727743167297
pancreasNCOA6chr203340310433403124GGT7chr203344382833443848
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 NCOA6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF992646NCOA69177203332928033329448NCOA6172271203332893033329029
AL706432PTTG1IP2488214627042446270910NCOA6485602203334577433345891
AA535712NDE11212161579699615797207NCOA6210400203330313033315213
BF572568ZNF3431812025050692505149NCOA680642203330286633324564
BF985843NCOA61192203333552833335720PPIL41774046149836664149836893

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 # sample3     2 1      1 
GAIN (# sample)2     2 1      1 
LOSS (# sample)1              1 
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=45

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=165)
Stat. for Synonymous SNVs
(# total SNVs=63)
Stat. for Deletions
(# total SNVs=5)
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
chr20:33345744-33345744p.Q269Q45
chr20:33329591-33329591p.S1490L4
chr20:33328653-33328653p.S1803P4
chr20:33330882-33330882p.P1060S3
chr20:33356323-33356323p.M153R3
chr20:33345899-33345899p.D218N3
chr20:33315155-33315155p.R2019Q3
chr20:33329288-33329288p.P1591L3
chr20:33345756-33345756p.Q265Q3
chr20:33328934-33328934p.S1709Y3

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample56 311 5 73 17105  2214121
# mutation56 311 6 83 21125  2515132
nonsynonymous SNV36 271 5 71 1575  219 25
synonymous SNV2  4  1 12 65   4617
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
chr20:33328653p.S1803P4
chr20:33345756p.Q265Q,NCOA63
chr20:33345759p.S535L,NCOA62
chr20:33330015p.P988T2
chr20:33330872p.S334F,NCOA62
chr20:33338167p.S1349T2
chr20:33345550p.Q275R,NCOA62
chr20:33345246p.S1490L2
chr20:33342596p.F435F,NCOA62
chr20:33345727p.Q264Q,NCOA62

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 NCOA6 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 NCOA6

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,SOGA1,AAR2,CEP250,CKAP5,DSN1,ITCH,
KIF3B,LOC647979,MOCS3,NCAPD3,NCOA6,NFS1,PHF20,
PIGU,PTPN1,RBM12,RBM39,TOP1,TRPC4AP,UQCC1
ANKRD17,AVL9,PRRC2C,BOD1L1,BPTF,CDK12,CDK13,
EP300,HEATR5B,KDM5A,LATS1,MGA,NCOA6,NF1,
NIPBL,RAD50,SETD2,SETD5,UBR5,WRN,ZNF318

ADNP,ARFGEF2,ASXL1,NOL4L,CEP250,DHX35,DIDO1,
HNF4A,ITCH,TTI1,KIF3B,LOC647979,NCOA3,NCOA6,
PHF20,RALGAPB,RPRD1B,STAU1,TAF4,TM9SF4,TRPC4AP
ANKRD52,ARID1A,BAZ2A,BIRC6,FOXO3B,GBF1,GOLGB1,
IGF2R,KDM2A,KIAA0368,KIAA2018,MYO18A,NCOA6,NCOR1,
PDPK1,PEAK1,TAF4,TCF20,UBN1,UBR4,ZFYVE26
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 NCOA6


There's no related Drug.
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Cross referenced IDs for NCOA6
* 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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