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 NCOA1

Basic gene info.	Gene symbol	NCOA1
	Gene name	nuclear receptor coactivator 1
	Synonyms	F-SRC-1\|KAT13A\|RIP160\|SRC1\|bHLHe42\|bHLHe74
	Cytomap	UCSC genome browser: 2p23
	Genomic location	chr2 :24807345-24993570
	Type of gene	protein-coding
	RefGenes	NM_003743.4, NM_147223.2,NM_147233.2,
	Ensembl id	ENSG00000084676
	Description	Hin-2 proteinPAX3/NCOA1 fusion proteinclass E basic helix-loop-helix protein 74renal carcinoma antigen NY-REN-52steroid receptor coactivator-1
	Modification date	20141207
dbXrefs	MIM : 602691
	HGNC : HGNC
	Ensembl : ENSG00000084676
	HPRD : 04070
	Vega : OTTHUMG00000125523
Protein	UniProt: Q15788 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NCOA1
	BioGPS: 8648
	Gene Expression Atlas: ENSG00000084676
	The Human Protein Atlas: ENSG00000084676
Pathway	NCI Pathway Interaction Database: NCOA1
	KEGG: NCOA1
	REACTOME: NCOA1
	ConsensusPathDB
	Pathway Commons: NCOA1
Metabolism	MetaCyc: NCOA1
	HUMANCyc: NCOA1
Regulation	Ensembl's Regulation: ENSG00000084676
	miRBase: chr2 :24,807,345-24,993,570
	TargetScan: NM_003743
	cisRED: ENSG00000084676
Context	iHOP: NCOA1
	cancer metabolism search in PubMed: NCOA1
	UCL Cancer Institute: NCOA1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOA1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	602691; gene. 602691; gene.
Orphanet
Disease	KEGG Disease: NCOA1
	MedGen: NCOA1 (Human Medical Genetics with Condition)
	ClinVar: NCOA1
Phenotype	MGI: NCOA1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	NCOA1	chr2	24833694	24833714	NCOA1	chr2	24847336	24847356
ovary	NCOA1	chr2	24853636	24853656	NCOA1	chr2	24854196	24854216
ovary	NCOA1	chr2	24920955	24920975	NCOA1	chr2	24935959	24935979
ovary	NCOA1	chr2	24923365	24923385	ATAD2B	chr2	24138735	24138755
ovary	NCOA1	chr2	24972212	24972232	NCOA1	chr2	24972282	24972302
pancreas	NCOA1	chr2	24813720	24813740		chr2	83447869	83447889
pancreas	NCOA1	chr2	24871174	24871194	NCOA1	chr2	24871357	24871377

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 NCOA1 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
AW204594	NCOA1	8	64	2	24930506	24930562	NCOA1	60	201	2	24930307	24930448
AY633656	PAX3	1	956	2	223085940	223163334	NCOA1	954	2861	2	24949456	24991385
AA319820	NCOA1	12	124	2	24992801	24992913	NCOA1	123	256	2	24992887	24993019
BX099622	NCOA1	1	104	2	24991741	24991843	NOVA1	91	309	14	27066721	27066939
BQ956364	PCGF3	1	165	4	702588	702753	NCOA1	157	719	2	24930064	24930624

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=3

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Somatic 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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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
chr2:24929877-24929877	p.S513L	2
chr2:24962316-24962316	p.R1073W	2
chr2:24974859-24974859	p.P1239S	2
chr2:24985555-24985555	p.?	2
chr2:24928097-24928097	p.I364I	2
chr2:24929991-24929991	p.S551F	2
chr2:24916179-24916179	p.T257T	2
chr2:24949464-24949464	p.P869H	2
chr2:24991150-24991150	p.D1406Y	1
chr2:24929854-24929854	p.N505N	1

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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=2

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	6	2	1	20	1		8		3	2		15	11	3			12	15	1	15
# mutation	8	2	1	22	1		8		3	2		15	12	3			14	18	1	22
nonsynonymous SNV	8	2	1	15	1		4		3			11	7	2			7	13		19
synonymous SNV				7			4			2		4	5	1			7	5	1	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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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
chr2:24974859	p.P1359P,NCOA1	2
chr2:24985567	p.P1239S,NCOA1	2
chr2:24930397	p.E1354Q,NCOA1	1
chr2:24952429	p.I363I,NCOA1	1
chr2:24888650	p.S513L,NCOA1	1
chr2:24928059	p.S729S,NCOA1	1
chr2:24929562	p.D887N,NCOA1	1
chr2:24930637	p.D75V,NCOA1	1
chr2:24964907	p.P1048P,NCOA1	1
chr2:24896324	p.D267G,NCOA1	1

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 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

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


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

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 NCOA1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q15788; -.
Chemistry	ChEMBL	CHEMBL2095162; -.
Chemistry	BindingDB	Q15788; -.
Chemistry	ChEMBL	CHEMBL2095162; -.
Organism-specific databases	PharmGKB	PA31470; -.
Organism-specific databases	PharmGKB	PA31470; -.
Organism-specific databases	CTD	8648; -.
Organism-specific databases	CTD	8648; -.

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
DB01645	nuclear receptor coactivator 1	experimental	Genistein
DB04652	nuclear receptor coactivator 1	experimental	(11-BETA)-11,21-DIHYDROXY-PREGN-4-ENE-3,20-DIONE
DB06832	nuclear receptor coactivator 1	experimental	2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL
DB06875	nuclear receptor coactivator 1	experimental	3-(3-FLUORO-4-HYDROXYPHENYL)-7-HYDROXY-1-NAPHTHONITRILE
DB06908	nuclear receptor coactivator 1	experimental	(2S)-3-(1-{[2-(2-CHLOROPHENYL)-5-METHYL-1,3-OXAZOL-4-YL]METHYL}-1H-INDOL-5-YL)-2-ETHOXYPROPANOIC ACID
DB06927	nuclear receptor coactivator 1	experimental	[5-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-YL]ACETONITRILE
DB07009	nuclear receptor coactivator 1	experimental	2-(5-HYDROXY-NAPHTHALEN-1-YL)-1,3-BENZOOXAZOL-6-OL
DB07080	nuclear receptor coactivator 1	experimental	N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE
DB07119	nuclear receptor coactivator 1	experimental	1-CHLORO-6-(4-HYDROXYPHENYL)-2-NAPHTHOL
DB07150	nuclear receptor coactivator 1	experimental	4-(4-HYDROXYPHENYL)-1-NAPHTHALDEHYDE OXIME
DB07198	nuclear receptor coactivator 1	experimental	5-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-CARBONITRILE
DB07215	nuclear receptor coactivator 1	experimental	2-METHYL-2-(4-{[({4-METHYL-2-[4-(TRIFLUOROMETHYL)PHENYL]-1,3-THIAZOL-5-YL}CARBONYL)AMINO]METHYL}PHENOXY)PROPANOIC ACID
DB07230	nuclear receptor coactivator 1	experimental	3-BROMO-6-HYDROXY-2-(4-HYDROXYPHENYL)-1H-INDEN-1-ONE
DB07236	nuclear receptor coactivator 1	experimental	3-(6-HYDROXY-NAPHTHALEN-2-YL)-BENZO[D]ISOOXAZOL-6-OL
DB07530	nuclear receptor coactivator 1	experimental	(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
DB07557	nuclear receptor coactivator 1	experimental	(5BETA)-PREGNANE-3,20-DIONE
DB07724	nuclear receptor coactivator 1	experimental	3-{5-methoxy-1-[(4-methoxyphenyl)sulfonyl]-1H-indol-3-yl}propanoic acid
DB08220	nuclear receptor coactivator 1	experimental	(8alpha,10alpha,13alpha,17beta)-17-[(4-hydroxyphenyl)carbonyl]androsta-3,5-diene-3-carboxylic acid
DB08231	nuclear receptor coactivator 1	experimental	MYRISTIC ACID
DB08483	nuclear receptor coactivator 1	experimental	(2S)-2-methoxy-3-{4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-1-benzothiophen-7-yl}propanoic acid
DB08742	nuclear receptor coactivator 1	experimental	1,3-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)
DB00755	nuclear receptor coactivator 1	approved; nutraceutical; investigational	Tretinoin

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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