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 CNOT4
Basic gene info.Gene symbolCNOT4
Gene nameCCR4-NOT transcription complex, subunit 4
SynonymsCLONE243|NOT4|NOT4H
CytomapUCSC genome browser: 7q33
Genomic locationchr7 :135071821-135194875
Type of geneprotein-coding
RefGenesNM_001008225.2,
NM_001190847.1,NM_001190848.1,NM_001190849.1,NM_001190850.1,
NM_013316.3,
Ensembl idENSG00000080802
DescriptionCCR4-NOT transcription complex subunit 4CCR4-associated factor 4E3 ubiquitin-protein ligase CNOT4NOT4 (negative regulator of transcription 4, yeast) homologpotential transcriptional repressor NOT4Hp
Modification date20141207
dbXrefs MIM : 604911
HGNC : HGNC
Ensembl : ENSG00000080802
HPRD : 05369
Vega : OTTHUMG00000155568
ProteinUniProt: O95628
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CNOT4
BioGPS: 4850
Gene Expression Atlas: ENSG00000080802
The Human Protein Atlas: ENSG00000080802
PathwayNCI Pathway Interaction Database: CNOT4
KEGG: CNOT4
REACTOME: CNOT4
ConsensusPathDB
Pathway Commons: CNOT4
MetabolismMetaCyc: CNOT4
HUMANCyc: CNOT4
RegulationEnsembl's Regulation: ENSG00000080802
miRBase: chr7 :135,071,821-135,194,875
TargetScan: NM_001008225
cisRED: ENSG00000080802
ContextiHOP: CNOT4
cancer metabolism search in PubMed: CNOT4
UCL Cancer Institute: CNOT4
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for CNOT4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CNOT4
Familial Cancer Database: CNOT4
* 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 604911; gene.
604911; gene.
Orphanet
DiseaseKEGG Disease: CNOT4
MedGen: CNOT4 (Human Medical Genetics with Condition)
ClinVar: CNOT4
PhenotypeMGI: CNOT4 (International Mouse Phenotyping Consortium)
PhenomicDB: CNOT4

Mutations for CNOT4
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryCNOT4chr7135101194135101214CNOT4chr7135078401135078421
ovaryCNOT4chr7135138101135138121CNOT4chr7135051715135051735
ovaryCNOT4chr7135159132135159152CNOT4chr7135159306135159326
pancreasCNOT4chr7135189205135189225CNOT4chr7135189524135189544
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 CNOT4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample        1 1      
GAIN (# sample)        1 1      
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)

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr7:135079001-135079001p.S429S3
chr7:135080547-135080547p.R320Q2
chr7:135098360-135098360p.A188A2
chr7:135122949-135122949p.R44Q2
chr7:135047695-135047695p.R621T2
chr7:135078943-135078943p.G449*1
chr7:135106938-135106938p.V113V1
chr7:135122994-135122994p.F29fs*501
chr7:135047761-135047761p.P599L1
chr7:135098328-135098328p.F199S1

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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
# sample2  5  3 2  65  1117 7
# mutation2  7  3 2  65  1116 9
nonsynonymous SNV2  4  3 1  64   93 7
synonymous SNV   3    1   1  123 2
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
chr7:135079001p.S429S,CNOT43
chr7:135106961p.V106I,CNOT42
chr7:135048771p.G556W,CNOT42
chr7:135080575p.P355Q,CNOT41
chr7:135100001p.V113V,CNOT41
chr7:135047860p.S574Y,CNOT41
chr7:135078869p.R320R,CNOT41
chr7:135082964p.V113I,CNOT41
chr7:135106934p.G556V,CNOT41
chr7:135047869p.N316T,CNOT41

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 CNOT4 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 CNOT4

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

CBLL1,CNOT4,COG5,KRIT1,LUZP6,MKLN1,MKRN1,
KMT2C,KMT2E,NAPEPLD,NUP205,RINT1,RSBN1L,TMEM209,
TNPO3,TTC26,UBE2H,UBN2,WASL,ZNF398,ZNF800
ARIH1,ARMC8,ATAD1,TRMT1L,CNOT4,DNAJC24,FAM175B,
CCSER2,FBXW11,POLR2M___GCOM1,KLHL24,LOC221710,NAA30,PCMTD1,
PPM1A,RCOR3,RPRD1A,SOS2,TAB2,TRIM23,TTC33

ATXN7L1,BRAF,CBLL1,CNOT4,EXOC4,GCC1,KLHDC10,
KRIT1,LUC7L2,LUZP6,MKLN1,KMT2C,KMT2E,RSBN1L,
SRPK2,TNPO3,TRIM4,UBN2,ZNF398,ZSCAN25,ZNF800
ARIH1,ASH1L,BAZ1B,CNOT4,DYNLL2,KIAA1429,KIDINS220,
KPNA6,LRCH3,KMT2A,KAT7,PIK3R4,RAB3GAP1,RSF1,
SETD1B,SNX27,UBR1,UBR5,ZNF37A,ZNF609,ZNF638
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 CNOT4


There's no related Drug.
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Cross referenced IDs for CNOT4
* 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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