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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 NCOR1

Basic gene info.	Gene symbol	NCOR1
	Gene name	nuclear receptor corepressor 1
	Synonyms	N-CoR\|N-CoR1\|PPP1R109\|TRAC1\|hN-CoR
	Cytomap	UCSC genome browser: 17p11.2
	Genomic location	chr17 :15933407-16097953
	Type of gene	protein-coding
	RefGenes	NM_001190438.1, NM_001190440.1,NM_006311.3,
	Ensembl id	ENSG00000141027
	Description	nuclear receptor co-repressor 1protein phosphatase 1, regulatory subunit 109thyroid hormone- and retinoic acid receptor-associated corepressor 1
	Modification date	20141207
dbXrefs	MIM : 600849
	HGNC : HGNC
	Ensembl : ENSG00000141027
	HPRD : 02911
	Vega : OTTHUMG00000059309
Protein	UniProt: O75376 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NCOR1
	BioGPS: 9611
	Gene Expression Atlas: ENSG00000141027
	The Human Protein Atlas: ENSG00000141027
Pathway	NCI Pathway Interaction Database: NCOR1
	KEGG: NCOR1
	REACTOME: NCOR1
	ConsensusPathDB
	Pathway Commons: NCOR1
Metabolism	MetaCyc: NCOR1
	HUMANCyc: NCOR1
Regulation	Ensembl's Regulation: ENSG00000141027
	miRBase: chr17 :15,933,407-16,097,953
	TargetScan: NM_001190438
	cisRED: ENSG00000141027
Context	iHOP: NCOR1
	cancer metabolism search in PubMed: NCOR1
	UCL Cancer Institute: NCOR1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOR1 in cancer cell metabolism	1. Fan W, Evans R (2015) PPARs and ERRs: molecular mediators of mitochondrial metabolism. Current opinion in cell biology 33: 49-54. go to article

Top

Phenotypic Information for NCOR1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NCOR1
	Familial Cancer Database: NCOR1

* 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 BRCA ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	600849; gene.
Orphanet
Disease	KEGG Disease: NCOR1
	MedGen: NCOR1 (Human Medical Genetics with Condition)
	ClinVar: NCOR1
Phenotype	MGI: NCOR1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NCOR1

Mutations for NCOR1

* 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

Top

- 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
haematopoietic_and_lymphoid_tissue	NCOR1	chr17	16013690	16013690	NCOR1	chr17	16013690	16013690
liver	NCOR1	chr17	15961715	15961715	NCOR1	chr17	16115434	16115434
liver	NCOR1	chr17	15961720	15961720	NCOR1	chr17	16115480	16115480

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 NCOR1 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
BM836125	NCOR1	10	273	17	16029416	16041526	SF3B1	266	360	2	198264798	198264892
BF961392	PHF21B	31	378	22	45280646	45280992	NCOR1	369	482	17	15945890	15946003
BU192483	TTC19	1	297	17	15928353	15930017	NCOR1	295	883	17	15935395	15938260
AW373603	NCOR1	16	274	17	16049710	16055297	RDX	269	550	11	110101812	110102093

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=7

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=190)	Stat. for Synonymous SNVs (# total SNVs=44)

Stat. for Deletions (# total SNVs=10)	Stat. for Insertions (# total SNVs=5)

Top

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
chr17:16068463-16068463	p.G150R	6
chr17:16089913-16089913	p.R66Q	5
chr17:16097825-16097825	p.Y20S	5
chr17:16068396-16068396	p.S172L	5
chr17:15995292-15995292	p.M967I	4
chr17:16097870-16097870	p.G5V	3
chr17:15973643-15973643	p.S1450L	3
chr17:15995176-15995176	p.?	3
chr17:15973527-15973527	p.Q1489E	3
chr17:16024504-16024504	p.R572*	3

Top

SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

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	9	11	2	33	2		10		11	3		15	8	1	1	4	18	21	2	21
# mutation	10	11	2	36	2		10		11	3		18	8	1	1	4	20	29	2	32
nonsynonymous SNV	9	9		28	2		9		7	2		15	5	1	1	3	18	20		23
synonymous SNV	1	2	2	8			1		4	1		3	3			1	2	9	2	9

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])

Top

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
chr17:15995292	p.M874I,NCOR1	4
chr17:15989674	p.P1097Q,NCOR1	2
chr17:15973548	p.I2132M,NCOR1	2
chr17:15968278	p.P1049P,NCOR1	2
chr17:15978996	p.R1498W,NCOR1	2
chr17:16012203	p.R1810Q,NCOR1	2
chr17:15965425	p.R1577Q,NCOR1	2
chr17:16068406	p.Q1190H,NCOR1	2
chr17:16068475	p.D37Y,NCOR1	2
chr17:15971267	p.E584D,NCOR1	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 NCOR1 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]

Top

Gene Expression for NCOR1

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


AKAP10,ANKFY1,ASXL2,BOD1L1,CLASP2,DMXL1,GIGYF2, HEATR5B,KDM3B,KIAA1109,KRBA2,MAP2K4,NCOR1,PAFAH1B1, RABEP1,RAPGEF6,REST,SMCR8,TTBK2,ZNF624,ZZEF1	AKAP9,HECTD4,CHD6,EP300,GIGYF2,HUWE1,LMTK2, MDN1,KAT6B,NCOA2,NCOR1,NSD1,PDPK1,REST, RSF1,SMCR8,TRRAP,ZKSCAN1,ZKSCAN8,ZNF445,ZNF827

ANKFY1,C17orf85,CAMTA2,CRK,FAM83G,FLII,FXR2, KDM6B,MINK1,NCOR1,PAFAH1B1,POLR2A,PRPF8,RABEP1, RAI1,RREB1,SMCR8,SMG6,TOP3A,VPS53,ZZEF1	ANKRD52,BAZ2A,BIRC6,PRR14L,CLTC,CNOT1,CSNK1G1, GBF1,GOLGB1,HIVEP1,IGF2R,MYO18A,NCOA6,NCOR1, PIK3C2B,RRBP1,RREB1,SAP130,TCF20,TRIM56,ZMIZ1

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for NCOR1

There's no related Drug.

Top

Cross referenced IDs for NCOR1

* 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