Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	NCOA6
	Gene name	nuclear receptor coactivator 6
	Synonyms	AIB3\|ASC2\|NRC\|PRIP\|RAP250\|TRBP
	Cytomap	UCSC genome browser: 20q11
	Genomic location	chr20 :33302577-33413433
	Type of gene	protein-coding
	RefGenes	NM_001242539.1, NM_014071.3,
	Ensembl id	ENSG00000198646
	Description	NRC 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 date	20141207
dbXrefs	MIM : 605299
	HGNC : HGNC
	Ensembl : ENSG00000198646
	HPRD : 05599
	Vega : OTTHUMG00000032311
Protein	UniProt: Q14686 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NCOA6
	BioGPS: 23054
	Gene Expression Atlas: ENSG00000198646
	The Human Protein Atlas: ENSG00000198646
Pathway	NCI Pathway Interaction Database: NCOA6
	KEGG: NCOA6
	REACTOME: NCOA6
	ConsensusPathDB
	Pathway Commons: NCOA6
Metabolism	MetaCyc: NCOA6
	HUMANCyc: NCOA6
Regulation	Ensembl's Regulation: ENSG00000198646
	miRBase: chr20 :33,302,577-33,413,433
	TargetScan: NM_001242539
	cisRED: ENSG00000198646
Context	iHOP: NCOA6
	cancer metabolism search in PubMed: NCOA6
	UCL Cancer Institute: NCOA6
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOA6 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	605299; gene.
Orphanet
Disease	KEGG Disease: NCOA6
	MedGen: NCOA6 (Human Medical Genetics with Condition)
	ClinVar: NCOA6
Phenotype	MGI: NCOA6 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	NCOA6	chr20	33332011	33332031		chr6	90601833	90601853
ovary	NCOA6	chr20	33397868	33397888	NCOA6	chr20	33398463	33398483
pancreas	NCOA6	chr20	33314279	33314299	CTCFL	chr20	56092786	56092806
pancreas	NCOA6	chr20	33319999	33320019	CTCFL	chr20	56088931	56088951
pancreas	NCOA6	chr20	33361158	33361178	ACSS2	chr20	33512160	33512180
pancreas	NCOA6	chr20	33375061	33375081	IFT52	chr20	42266155	42266175
pancreas	NCOA6	chr20	33381251	33381271		chr20	56101793	56101813
pancreas	NCOA6	chr20	33393519	33393539	MIR5095	chr20	55926472	55926492
pancreas	NCOA6	chr20	33402436	33402456	PKIG	chr20	43167277	43167297
pancreas	NCOA6	chr20	33403104	33403124	GGT7	chr20	33443828	33443848

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NCOA6 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
BF992646	NCOA6	9	177	20	33329280	33329448	NCOA6	172	271	20	33328930	33329029
AL706432	PTTG1IP	2	488	21	46270424	46270910	NCOA6	485	602	20	33345774	33345891
AA535712	NDE1	1	212	16	15796996	15797207	NCOA6	210	400	20	33303130	33315213
BF572568	ZNF343	1	81	20	2505069	2505149	NCOA6	80	642	20	33302866	33324564
BF985843	NCOA6	1	192	20	33335528	33335720	PPIL4	177	404	6	149836664	149836893

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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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
chr20:33345744-33345744	p.Q269Q	45
chr20:33329591-33329591	p.S1490L	4
chr20:33328653-33328653	p.S1803P	4
chr20:33330882-33330882	p.P1060S	3
chr20:33356323-33356323	p.M153R	3
chr20:33345899-33345899	p.D218N	3
chr20:33315155-33315155	p.R2019Q	3
chr20:33329288-33329288	p.P1591L	3
chr20:33345756-33345756	p.Q265Q	3
chr20:33328934-33328934	p.S1709Y	3

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	5	6		31	1		5		7	3		17	10	5			22	14	1	21
# mutation	5	6		31	1		6		8	3		21	12	5			25	15	1	32
nonsynonymous SNV	3	6		27	1		5		7	1		15	7	5			21	9		25
synonymous SNV	2			4			1		1	2		6	5				4	6	1	7

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
chr20:33328653	p.S1803P	4
chr20:33345756	p.Q265Q,NCOA6	3
chr20:33345759	p.R1026Q,NCOA6	2
chr20:33330015	p.S535L,NCOA6	2
chr20:33330872	p.P988T	2
chr20:33338167	p.S334F,NCOA6	2
chr20:33345550	p.S1349T	2
chr20:33345246	p.Q275R,NCOA6	2
chr20:33342596	p.S1490L	2
chr20:33345727	p.Q264Q,NCOA6	2

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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