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 CNOT2
Basic gene info.Gene symbolCNOT2
Gene nameCCR4-NOT transcription complex, subunit 2
SynonymsCDC36|NOT2|NOT2H
CytomapUCSC genome browser: 12q15
Genomic locationchr12 :70637493-70748773
Type of geneprotein-coding
RefGenesNM_001199302.1,
NM_001199303.1,NM_014515.5,NR_037615.1,
Ensembl idENSG00000111596
DescriptionCCR4-NOT transcription complex subunit 2CCR4-associated factor 2negative regulator of transcription 2
Modification date20141207
dbXrefs MIM : 604909
HGNC : HGNC
Ensembl : ENSG00000111596
HPRD : 05367
Vega : OTTHUMG00000169481
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CNOT2
BioGPS: 4848
Gene Expression Atlas: ENSG00000111596
The Human Protein Atlas: ENSG00000111596
PathwayNCI Pathway Interaction Database: CNOT2
KEGG: CNOT2
REACTOME: CNOT2
ConsensusPathDB
Pathway Commons: CNOT2
MetabolismMetaCyc: CNOT2
HUMANCyc: CNOT2
RegulationEnsembl's Regulation: ENSG00000111596
miRBase: chr12 :70,637,493-70,748,773
TargetScan: NM_001199302
cisRED: ENSG00000111596
ContextiHOP: CNOT2
cancer metabolism search in PubMed: CNOT2
UCL Cancer Institute: CNOT2
Assigned class in ccmGDBC

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Phenotypic Information for CNOT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CNOT2
Familial Cancer Database: CNOT2
* 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_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CNOT2
MedGen: CNOT2 (Human Medical Genetics with Condition)
ClinVar: CNOT2
PhenotypeMGI: CNOT2 (International Mouse Phenotyping Consortium)
PhenomicDB: CNOT2

Mutations for CNOT2
* 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
ovaryCNOT2chr127065045070650470chr152782511327825133
ovaryCNOT2chr127065951170659531CNOT2chr127065927070659290
ovaryCNOT2chr127068182170681841CNOT2chr127068195370681973
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 CNOT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA071465FAU2274116488810264888154CNOT266491127074771570748140
AF130057CNOT212594127071546170718054AHSG258428603186338832186339107
BC008476PCDH911019136774843267749456CNOT210181205127067726670677455

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 # sample32    1 1    12  
GAIN (# sample)32      1    12  
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=54)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr12:70723257-70723257p.R98H4
chr12:70747693-70747693p.*541K3
chr12:70724190-70724190p.S170S3
chr12:70724078-70724078p.P133L2
chr12:70704744-70704744p.E40K2
chr12:70747694-70747694p.*541fs?2
chr12:70739968-70739968p.R467H2
chr12:70704760-70704760p.S45N2
chr12:70723292-70723292p.V110I2
chr12:70723313-70723313p.P117T2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 51   11 541  34110
# mutation 2 62   11 641  34110
nonsynonymous SNV 2 42   1  431  24 7
synonymous SNV   2     1 21   1 13
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
chr12:70724190p.S170S,CNOT23
chr12:70704760p.S45N,CNOT22
chr12:70723292p.V110I,CNOT22
chr12:70735907p.A400V,CNOT22
chr12:70672044p.R13I,CNOT22
chr12:70723272p.F186F,CNOT21
chr12:70732228p.S47P,CNOT21
chr12:70704758p.G203E,CNOT21
chr12:70723291p.E55K,CNOT21
chr12:70732251p.S207F,CNOT21

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 CNOT2 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 CNOT2

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

CAND1,CCT2,CNOT2,CPSF6,DEFB128,FRS2,LEMD3,
MDM1,MDM2,NUP107,RAB21,RAB3IP,RAP1B,SLC35E3,
TBC1D15,TBK1,THAP2,TMBIM4,TMEM19,YEATS4,ZFC3H1
CAND1,CCDC60,CNOT2,DCAF10,DQX1,ELAVL3,FRS2,
GRIP1,HELB,ITFG1,LOC653544,MDM2,MS4A8,NUP107,
OR4F17,RAB3IP,SLC35E3,VPS35,YEATS4,ZFC3H1,ZMYM2

ACTR6,ATXN7L3B,BRAP,CAND1,CNOT2,CPSF6,DENR,
FBXO21,FRS2,KIAA1033,KRR1,METAP2,PLEKHA5,PRDM4,
RAB3IP,RNF34,SCYL2,SCAF11,TDG,VEZT,ZNF664
ACTR2,CNOT11,CMAS,CNOT2,CXorf56,EXOC1,GDAP2,
GPBP1,IFT74,C2CD5,LACTB,MTF2,NLK,NSUN3,
PGGT1B,PPP2R5A,PWWP2A,RAB14,RFFL,SLC38A9,TBL1XR1
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 CNOT2


There's no related Drug.
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Cross referenced IDs for CNOT2
* 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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