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 NCOR2

Basic gene info.	Gene symbol	NCOR2
	Gene name	nuclear receptor corepressor 2
	Synonyms	CTG26\|N-CoR2\|SMAP270\|SMRT\|SMRTE\|SMRTE-tau\|TNRC14\|TRAC\|TRAC-1\|TRAC1
	Cytomap	UCSC genome browser: 12q24
	Genomic location	chr12 :124808956-125052010
	Type of gene	protein-coding
	RefGenes	NM_001077261.3, NM_001206654.1,NM_006312.5,
	Ensembl id	ENSG00000196498
	Description	CTG repeat protein 26T3 receptor-associating factorsilencing mediator for retinoid and thyroid hormone receptorsthyroid-, retinoic-acid-receptor-associated corepressor
	Modification date	20141207
dbXrefs	MIM : 600848
	HGNC : HGNC
	Ensembl : ENSG00000196498
	HPRD : 02910
	Vega : OTTHUMG00000150455
Protein	UniProt: Q9Y618 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NCOR2
	BioGPS: 9612
	Gene Expression Atlas: ENSG00000196498
	The Human Protein Atlas: ENSG00000196498
Pathway	NCI Pathway Interaction Database: NCOR2
	KEGG: NCOR2
	REACTOME: NCOR2
	ConsensusPathDB
	Pathway Commons: NCOR2
Metabolism	MetaCyc: NCOR2
	HUMANCyc: NCOR2
Regulation	Ensembl's Regulation: ENSG00000196498
	miRBase: chr12 :124,808,956-125,052,010
	TargetScan: NM_001077261
	cisRED: ENSG00000196498
Context	iHOP: NCOR2
	cancer metabolism search in PubMed: NCOR2
	UCL Cancer Institute: NCOR2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for NCOR2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NCOR2
	Familial Cancer Database: NCOR2

* 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	600848; gene.
Orphanet
Disease	KEGG Disease: NCOR2
	MedGen: NCOR2 (Human Medical Genetics with Condition)
	ClinVar: NCOR2
Phenotype	MGI: NCOR2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NCOR2

Mutations for NCOR2

* 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	NCOR2	chr12	124837932	124837952	CCDC60	chr12	119851154	119851174
ovary	NCOR2	chr12	124940352	124940372	TMEM132B	chr12	125920636	125920656
ovary	NCOR2	chr12	124970841	124970861	SIGLEC7	chr19	51646698	51646718
ovary	NCOR2	chr12	125040852	125040872		chr12	125052039	125052059
prostate	NCOR2	chr12	124835961	124837961		chr18	38104992	38106992
prostate	NCOR2	chr12	124857801	124857801	NCOR2	chr12	124857936	124857936
soft_tissue	NCOR2	chr12	124901263	124901263	PGAM5	chr12	133293628	133293628

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 NCOR2 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
BF528779	SLC4A5	1	64	2	74590152	74590215	NCOR2	60	642	12	124824634	124826533
BF803065	NCOR2	17	235	12	124885053	124887000	OTUD5	227	376	X	48801477	48814320
BC020427	SLC4A5	1	65	2	74590152	74590216	NCOR2	61	1362	12	124819776	124826533
AA580941	NCOR2	8	63	12	124868037	124868092	FBXO33	62	325	14	39896063	39896326
BF093171	TLN1	1	353	9	35697622	35698100	NCOR2	339	510	12	124943923	124944094
BC051312	NCOR2	1	1589	12	124904505	124979906	RPL14	1589	1817	3	40503539	40503767
BC033087	NCOR2	1	1752	12	124904505	125002840	RPL14	1752	1975	3	40503542	40503765
BF924756	CHN1	61	173	2	175673268	175673586	NCOR2	169	380	12	124956726	124956937
U37146	HNRNPK	1	530	9	86585117	86586958	NCOR2	529	5971	12	124808961	124841329
BF846253	MALAT1	1	63	11	65268026	65268091	NCOR2	46	259	12	124887007	124904603

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=13

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=119)	Stat. for Synonymous SNVs (# total SNVs=87)

Stat. for Deletions (# total SNVs=15)	Stat. for Insertions (# total SNVs=43)

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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
chr12:124824721-124824722	p.G1849_G1850insSSG	16
chr12:124887093-124887093	p.Q499Q	13
chr12:124887058-124887059	p.Q510_P511insQ	13
chr12:124829255-124829255	p.G1541G	8
chr12:124824739-124824740	p.S1841fs*197	7
chr12:124848228-124848228	p.I976fs*94	6
chr12:124887099-124887099	p.Q497Q	4
chr12:124829234-124829234	p.L1548L	3
chr12:124856618-124856618	p.A919A	2
chr12:124821373-124821373	p.P2021L	2

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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=17

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	4		30	1		11		8	2		24	11	2	2		29	24	2	21
# mutation	6	4		33	1		12		7	2		27	12	2	1		37	30	1	37
nonsynonymous SNV	6	3		19	1		9		4			18	7	1			23	22		23
synonymous SNV		1		14			3		3	2		9	5	1	1		14	8	1	14

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
chr12:124887093	p.Q498Q,NCOR2	17
chr12:124821373	p.S2004L,NCOR2	2
chr12:124887004	p.A528E,NCOR2	2
chr12:124950753	p.R315H,NCOR2	2
chr12:124887099	p.Q496Q,NCOR2	2
chr12:124904522	p.R487Q,NCOR2	2
chr12:124840068	p.P1087P,NCOR2	2
chr12:124915272	p.R224H,NCOR2	2
chr12:124839417	p.G708G,NCOR2	1
chr12:124856705	p.R1661R,NCOR2	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 NCOR2 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 NCOR2

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


IRF2BPL,CIC,CXXC5,DDX54,EP400,GATC,HCFC1, LTBP3,NCOR2,NISCH,PHRF1,PKD1,PRR12,RAI1, RFX1,RILPL1,SETD1B,TLE3,TNRC18,ULK1,WDR81	AHDC1,ATG2A,PRRC2A,CHERP,CUL7,DHX30,DHX37, GTPBP1,INTS1,KDM5C,KHSRP,MYBBP1A,NCOR2,PHRF1, PRR12,RAI1,SCRIB,SETD1A,TNRC18,TSC2,ZNF777

PRRC2B,HECTD4,CIC,CLIP1,CREBBP,CTDSP2,EP400, ARHGAP35,HSPG2,LRP1,MAPKBP1,MED13L,KMT2B___KMT2D,MYO9B, NCOR2,PRR12,RAPGEF1,SETD1B,SKI,SSH1,TRIM56	HECTD4,CIC,CREBBP,DIDO1,DYNC1H1,EP300,FAM193A, STRIP1,FLII,HERC2,MYO1C,NCOR2,PI4KA,PRR12, RERE,SCAF1,SETD1A,SMG6,TNRC18,TNRC6C,UBTF

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 NCOR2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q9Y618; -.
Chemistry	ChEMBL	CHEMBL2096976; -.
Organism-specific databases	PharmGKB	PA31478; -.
Organism-specific databases	CTD	9612; -.

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
DB00755	nuclear receptor corepressor 2	approved; nutraceutical; investigational	Tretinoin
DB01001	nuclear receptor corepressor 2	approved	Salbutamol

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Cross referenced IDs for NCOR2

* 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