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 NCOR1
Basic gene info.Gene symbolNCOR1
Gene namenuclear receptor corepressor 1
SynonymsN-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR
CytomapUCSC genome browser: 17p11.2
Genomic locationchr17 :15933407-16097953
Type of geneprotein-coding
RefGenesNM_001190438.1,
NM_001190440.1,NM_006311.3,
Ensembl idENSG00000141027
Descriptionnuclear receptor co-repressor 1protein phosphatase 1, regulatory subunit 109thyroid hormone- and retinoic acid receptor-associated corepressor 1
Modification date20141207
dbXrefs MIM : 600849
HGNC : HGNC
Ensembl : ENSG00000141027
HPRD : 02911
Vega : OTTHUMG00000059309
ProteinUniProt: O75376
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NCOR1
BioGPS: 9611
Gene Expression Atlas: ENSG00000141027
The Human Protein Atlas: ENSG00000141027
PathwayNCI Pathway Interaction Database: NCOR1
KEGG: NCOR1
REACTOME: NCOR1
ConsensusPathDB
Pathway Commons: NCOR1
MetabolismMetaCyc: NCOR1
HUMANCyc: NCOR1
RegulationEnsembl's Regulation: ENSG00000141027
miRBase: chr17 :15,933,407-16,097,953
TargetScan: NM_001190438
cisRED: ENSG00000141027
ContextiHOP: NCOR1
cancer metabolism search in PubMed: NCOR1
UCL Cancer Institute: NCOR1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOR1 in cancer cell metabolism1. Fan W, Evans R (2015) PPARs and ERRs: molecular mediators of mitochondrial metabolism. Current opinion in cell biology 33: 49-54. go to article

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Phenotypic Information for NCOR1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 600849; gene.
Orphanet
DiseaseKEGG Disease: NCOR1
MedGen: NCOR1 (Human Medical Genetics with Condition)
ClinVar: NCOR1
PhenotypeMGI: NCOR1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
haematopoietic_and_lymphoid_tissueNCOR1chr171601369016013690NCOR1chr171601369016013690
liverNCOR1chr171596171515961715NCOR1chr171611543416115434
liverNCOR1chr171596172015961720NCOR1chr171611548016115480
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NCOR1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM836125NCOR110273171602941616041526SF3B12663602198264798198264892
BF961392PHF21B31378224528064645280992NCOR1369482171594589015946003
BU192483TTC191297171592835315930017NCOR1295883171593539515938260
AW373603NCOR116274171604971016055297RDX26955011110101812110102093

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2     5 1     2 1
GAIN (# sample)                 
LOSS (# sample)2     5 1     2 1
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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check002.gifSNV 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

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check002.gifSomatic 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)

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr17:16068463-16068463p.G150R6
chr17:16068396-16068396p.S172L5
chr17:16097825-16097825p.Y20S5
chr17:16089913-16089913p.R66Q5
chr17:15995292-15995292p.M967I4
chr17:15995176-15995176p.?3
chr17:15973643-15973643p.S1450L3
chr17:16097870-16097870p.G5V3
chr17:15973527-15973527p.Q1489E3
chr17:15965543-15965543p.R1755C3

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample9112332 10 113 1581141821221
# mutation10112362 10 113 1881142029232
nonsynonymous SNV99 282 9 72 1551131820 23
synonymous SNV1228  1 41 33  12929
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr17:15995292p.M874I,NCOR14
chr17:15973548p.M874V,NCOR12
chr17:15989674p.Q60E,NCOR12
chr17:15968278p.G1685G,NCOR12
chr17:15978996p.I2132M,NCOR12
chr17:16012203p.P1097Q,NCOR12
chr17:15965425p.P1049P,NCOR12
chr17:16068406p.R1498W,NCOR12
chr17:16068475p.R1810Q,NCOR12
chr17:15971267p.R1577Q,NCOR12

check002.gifOther 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

check002.gifCopy 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]

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Gene Expression for NCOR1

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 NCOR1


There's no related Drug.
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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



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