Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolNCOR2
Gene namenuclear receptor corepressor 2
SynonymsCTG26|N-CoR2|SMAP270|SMRT|SMRTE|SMRTE-tau|TNRC14|TRAC|TRAC-1|TRAC1
CytomapUCSC genome browser: 12q24
Genomic locationchr12 :124808956-125052010
Type of geneprotein-coding
RefGenesNM_001077261.3,
NM_001206654.1,NM_006312.5,
Ensembl idENSG00000196498
DescriptionCTG repeat protein 26T3 receptor-associating factorsilencing mediator for retinoid and thyroid hormone receptorsthyroid-, retinoic-acid-receptor-associated corepressor
Modification date20141207
dbXrefs MIM : 600848
HGNC : HGNC
Ensembl : ENSG00000196498
HPRD : 02910
Vega : OTTHUMG00000150455
ProteinUniProt: Q9Y618
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NCOR2
BioGPS: 9612
Gene Expression Atlas: ENSG00000196498
The Human Protein Atlas: ENSG00000196498
PathwayNCI Pathway Interaction Database: NCOR2
KEGG: NCOR2
REACTOME: NCOR2
ConsensusPathDB
Pathway Commons: NCOR2
MetabolismMetaCyc: NCOR2
HUMANCyc: NCOR2
RegulationEnsembl's Regulation: ENSG00000196498
miRBase: chr12 :124,808,956-125,052,010
TargetScan: NM_001077261
cisRED: ENSG00000196498
ContextiHOP: NCOR2
cancer metabolism search in PubMed: NCOR2
UCL Cancer Institute: NCOR2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for NCOR2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 600848; gene.
Orphanet
DiseaseKEGG Disease: NCOR2
MedGen: NCOR2 (Human Medical Genetics with Condition)
ClinVar: NCOR2
PhenotypeMGI: NCOR2 (International Mouse Phenotyping Consortium)
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.

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
ovaryNCOR2chr12124837932124837952CCDC60chr12119851154119851174
ovaryNCOR2chr12124940352124940372TMEM132Bchr12125920636125920656
ovaryNCOR2chr12124970841124970861SIGLEC7chr195164669851646718
ovaryNCOR2chr12125040852125040872chr12125052039125052059
prostateNCOR2chr12124835961124837961chr183810499238106992
prostateNCOR2chr12124857801124857801NCOR2chr12124857936124857936
soft_tissueNCOR2chr12124901263124901263PGAM5chr12133293628133293628
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 NCOR2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF528779SLC4A516427459015274590215NCOR26064212124824634124826533
BF803065NCOR21723512124885053124887000OTUD5227376X4880147748814320
BC020427SLC4A516527459015274590216NCOR261136212124819776124826533
AA580941NCOR286312124868037124868092FBXO3362325143989606339896326
BF093171TLN1135393569762235698100NCOR233951012124943923124944094
BC051312NCOR21158912124904505124979906RPL141589181734050353940503767
BC033087NCOR21175212124904505125002840RPL141752197534050354240503765
BF924756CHN1611732175673268175673586NCOR216938012124956726124956937
U37146HNRNPK153098658511786586958NCOR2529597112124808961124841329
BF846253MALAT1163116526802665268091NCOR24625912124887007124904603

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 # sample1                
GAIN (# sample)                 
LOSS (# sample)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=13

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check002.gifSomatic 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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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
chr12:124824721-124824722p.G1849_G1850insSSG16
chr12:124887093-124887093p.Q499Q13
chr12:124887058-124887059p.Q510_P511insQ13
chr12:124829255-124829255p.G1541G8
chr12:124824739-124824740p.S1841fs*1977
chr12:124848228-124848228p.I976fs*946
chr12:124887099-124887099p.Q497Q4
chr12:124829234-124829234p.L1548L3
chr12:124820028-124820028p.?2
chr12:124856618-124856618p.A919A2

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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=17

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample64 301 11 82 241122 2924221
# mutation64 331 12 72 271221 3730137
nonsynonymous SNV63 191 9 4  1871  2322 23
synonymous SNV 1 14  3 32 9511 148114
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
chr12:124887093p.Q498Q,NCOR217
chr12:124915272p.S2004L,NCOR22
chr12:124821373p.A528E,NCOR22
chr12:124887004p.R315H,NCOR22
chr12:124950753p.Q496Q,NCOR22
chr12:124887099p.R487Q,NCOR22
chr12:124904522p.P1087P,NCOR22
chr12:124840068p.R224H,NCOR22
chr12:124835278p.D540N,NCOR21
chr12:124856641p.L1423P,NCOR21

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 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

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

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
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 NCOR2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q9Y618; -.
ChemistryChEMBL CHEMBL2096976; -.
Organism-specific databasesPharmGKB PA31478; -.
Organism-specific databasesCTD 9612; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00755nuclear receptor corepressor 2approved; nutraceutical; investigationalTretinoin
DB01001nuclear receptor corepressor 2approvedSalbutamol


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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



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