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 NCOA3

Basic gene info.	Gene symbol	NCOA3
	Gene name	nuclear receptor coactivator 3
	Synonyms	ACTR\|AIB-1\|AIB1\|CAGH16\|CTG26\|KAT13B\|RAC3\|SRC-3\|SRC3\|TNRC14\|TNRC16\|TRAM-1\|bHLHe42\|pCIP
	Cytomap	UCSC genome browser: 20q12
	Genomic location	chr20 :46130600-46285621
	Type of gene	protein-coding
	RefGenes	NM_001174087.1, NM_001174088.1,NM_006534.3,NM_181659.2,
	Ensembl id	ENSG00000124151
	Description	CBP-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 date	20141207
dbXrefs	MIM : 601937
	HGNC : HGNC
	Ensembl : ENSG00000124151
	HPRD : 03570
	Vega : OTTHUMG00000033061
Protein	UniProt: Q9Y6Q9 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NCOA3
	BioGPS: 8202
	Gene Expression Atlas: ENSG00000124151
	The Human Protein Atlas: ENSG00000124151
Pathway	NCI Pathway Interaction Database: NCOA3
	KEGG: NCOA3
	REACTOME: NCOA3
	ConsensusPathDB
	Pathway Commons: NCOA3
Metabolism	MetaCyc: NCOA3
	HUMANCyc: NCOA3
Regulation	Ensembl's Regulation: ENSG00000124151
	miRBase: chr20 :46,130,600-46,285,621
	TargetScan: NM_001174087
	cisRED: ENSG00000124151
Context	iHOP: NCOA3
	cancer metabolism search in PubMed: NCOA3
	UCL Cancer Institute: NCOA3
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOA3 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	601937; gene. 601937; gene.
Orphanet
Disease	KEGG Disease: NCOA3
	MedGen: NCOA3 (Human Medical Genetics with Condition)
	ClinVar: NCOA3
Phenotype	MGI: NCOA3 (International Mouse Phenotyping Consortium)
Phenotype	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.

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	NCOA3	chr20	46158748	46158768		chr22	38294210	38294230
ovary	NCOA3	chr20	46206475	46206495	NCOA3	chr20	46200684	46200704
ovary	NCOA3	chr20	46251918	46251938	NCOA3	chr20	46197824	46197844
ovary	NCOA3	chr20	46261851	46261871	SULF2	chr20	46340708	46340728
ovary	NCOA3	chr20	46261852	46261872	SULF2	chr20	46340708	46340728
pancreas	NCOA3	chr20	46138721	46138741		chr20	46078459	46078479
pancreas	NCOA3	chr20	46213968	46213988		chr15	77208146	77208166

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 NCOA3 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
DA523336	NCOA3	1	109	20	46130657	46130765	SLAIN1	106	549	13	78293665	78318569
DB144841	NCOA3	1	107	20	46130657	46130763	TXNDC5	106	547	6	7899876	8002806
BQ009202	C4orf48	18	285	4	2044137	2045691	NCOA3	283	698	20	46275876	46279816
BF839348	ANTXR1	9	234	2	69350198	69397409	NCOA3	229	372	20	46219171	46219314
BP292769	STAT5B	1	496	17	40359571	40362610	NCOA3	493	552	20	46269913	46269972
DA853259	NCOA3	4	139	20	46130628	46130763	ZMYND8	138	570	20	45920609	45938950
F12469	NCOA3	1	114	20	46132899	46133012	CD36	112	152	7	80125707	80125747
BE832543	XPO6	1	112	16	28157506	28164073	NCOA3	112	188	20	46265422	46265498
AI571643	SPINK1	1	233	5	147204146	147207693	NCOA3	225	406	20	46232662	46232843

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=17

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Somatic 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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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
chr20:46279837-46279839	p.Q1255delQ	17
chr20:46279860-46279860	p.Q1262Q	12
chr20:46279830-46279830	p.Q1252Q	6
chr20:46279839-46279839	p.Q1255Q	6
chr20:46279827-46279827	p.Q1251Q	5
chr20:46279836-46279836	p.Q1254Q	5
chr20:46264449-46264449	p.P499L	4
chr20:46279834-46279836	p.Q1254delQ	4
chr20:46265284-46265284	p.D718D	3
chr20:46279866-46279866	p.Q1264Q	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=3

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	8	1	20	2		6		4	1		13	4	4			15	17	1	12
# mutation	5	8	1	21	2		6		4	1		16	4	4			15	18	1	13
nonsynonymous SNV	4	8	1	15	1		4		4	1		11	4	3			12	12	1	10
synonymous SNV	1			6	1		2					5		1			3	6		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
chr20:46279860	p.Q1261Q,NCOA3	3
chr20:46264449	p.P499H,NCOA3	3
chr20:46281213	p.F1279F,NCOA3	2
chr20:46255881	p.A1303T,NCOA3	2
chr20:46281693	p.P499P,NCOA3	2
chr20:46279914	p.D165N,NCOA3	2
chr20:46279984	p.S1336L,NCOA3	2
chr20:46265284	p.D718D,NCOA3	2
chr20:46264450	p.Q1379Q,NCOA3	2
chr20:46275921	p.L804F,NCOA3	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 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

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,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

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 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