Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 CNOT8
Basic gene info.Gene symbolCNOT8
Gene nameCCR4-NOT transcription complex, subunit 8
SynonymsCAF1|CALIF|Caf1b|POP2|hCAF1
CytomapUCSC genome browser: 5q31-q33
Genomic locationchr5 :154238197-154256352
Type of geneprotein-coding
RefGenesNM_001301073.1,
NM_001301074.1,NM_001301075.1,NM_001301077.1,NM_001301080.1,
NM_001301082.1,NM_001301083.1,NM_001301086.1,NM_004779.5,
Ensembl idENSG00000155508
DescriptionCAF1-like proteinCAF2CALIFpCCR4-NOT transcription complex subunit 8CCR4-associated factor 8PGK promoter directed over production
Modification date20141207
dbXrefs MIM : 603731
HGNC : HGNC
Ensembl : ENSG00000155508
HPRD : 07225
Vega : OTTHUMG00000130192
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CNOT8
BioGPS: 9337
Gene Expression Atlas: ENSG00000155508
The Human Protein Atlas: ENSG00000155508
PathwayNCI Pathway Interaction Database: CNOT8
KEGG: CNOT8
REACTOME: CNOT8
ConsensusPathDB
Pathway Commons: CNOT8
MetabolismMetaCyc: CNOT8
HUMANCyc: CNOT8
RegulationEnsembl's Regulation: ENSG00000155508
miRBase: chr5 :154,238,197-154,256,352
TargetScan: NM_001301073
cisRED: ENSG00000155508
ContextiHOP: CNOT8
cancer metabolism search in PubMed: CNOT8
UCL Cancer Institute: CNOT8
Assigned class in ccmGDBC

Top
Phenotypic Information for CNOT8(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CNOT8
Familial Cancer Database: CNOT8
* 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: CNOT8
MedGen: CNOT8 (Human Medical Genetics with Condition)
ClinVar: CNOT8
PhenotypeMGI: CNOT8 (International Mouse Phenotyping Consortium)
PhenomicDB: CNOT8

Mutations for CNOT8
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CNOT8 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE720800MALAT110110116526801465268112CNOT8932955154242795154244793
AW015591JUND1142191839098718391128CNOT81372965154238456154238615
BG979616PLEKHA6131901204210536204210919CNOT81853115154240133154240259
BF901254CNOT8113695154244520154244876GOLGB13614653121411199121411303
BF063953JUND1144191839098618391128CNOT81393975154238357154238615

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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=2

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

Top
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
chr5:154254952-154254952p.Q278*2
chr5:154252176-154252176p.L232fs*21
chr5:154242937-154242937p.S33S1
chr5:154250249-154250249p.D114Y1
chr5:154252212-154252212p.?1
chr5:154244779-154244779p.R49*1
chr5:154250262-154250262p.N118I1
chr5:154254880-154254880p.K254*1
chr5:154244809-154244809p.D59Y1
chr5:154250333-154250333p.T142S1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 11 2    1     1 3
# mutation11 11 2    1     1 3
nonsynonymous SNV11 11 2          1 3
synonymous SNV           1        
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
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
chr5:154250226p.D106G2
chr5:154250228p.M107V1
chr5:154250259p.A117V1
chr5:154250262p.N118I1
chr5:154250340p.G144E1
chr5:154251334p.R173H1
chr5:154251380p.F188L1
chr5:154252115p.E211D1
chr5:154254903p.G261G1
chr5:154254920p.A267V1

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 CNOT8 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 CNOT8

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))
Top
check002.gifCNV 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
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

C5orf15,CEP120,CNOT8,CSNK1A1,CSNK1G3,DCTN4,FAM114A2,
FBXL17,FBXO38,GIN1,KDM3B,MATR3,MFAP3,PGGT1B,
PJA2,PWWP2A,RBM22,RBM27,SLU7,SMAD5,ZCCHC10
ATG5,BET1,CMPK1,CNOT8,DTWD1,EXOC1,GOLPH3,
NUP54,NXT2,PAPD4,PDCD10,SMAD2,SPTLC1,SSR1,
TCEA1,TMEM128,TMEM167B,TMEM50A,UFM1,VPS26A,YIPF5

C5orf24,TRAPPC13,CNOT8,CRBN,FBXO38,HINT1,MAT2B,
MATR3,MED7,RBM22,RNF14,RPS14,SREK1IP1,SKP1,
SLU7,SRP9,TAF7,TTC1,UBE2B,ZCCHC10,ZNF627
ASF1A,DHRS4-AS1,METTL23,C6orf57,TRIQK,CLNS1A,CNOT8,
CRLS1,DUSP11,EBAG9,FAM60A,ISCA2,LIAS,NXT2,
PEX11B,RCHY1,SLC35A1,TBPL1,TGDS,TMEM69,TXNDC12
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for CNOT8
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01033CCR4-NOT transcription complex, subunit 8approvedMercaptopurine
DB00563CCR4-NOT transcription complex, subunit 8approvedMethotrexate


Top
Cross referenced IDs for CNOT8
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas