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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CNOT6 |
Basic gene info. | Gene symbol | CNOT6 |
Gene name | CCR4-NOT transcription complex, subunit 6 | |
Synonyms | CCR4|Ccr4a | |
Cytomap | UCSC genome browser: 5q35.3 | |
Genomic location | chr5 :179921416-180005353 | |
Type of gene | protein-coding | |
RefGenes | NM_015455.3, | |
Ensembl id | ENSG00000113300 | |
Description | CCR4-NOT transcription complex subunit 6carbon catabolite repression 4 proteincarbon catabolite repressor protein 4 homologcytoplasmic deadenylase | |
Modification date | 20141207 | |
dbXrefs | MIM : 608951 | |
HGNC : HGNC | ||
Ensembl : ENSG00000113300 | ||
HPRD : 12341 | ||
Vega : OTTHUMG00000130935 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CNOT6 | |
BioGPS: 57472 | ||
Gene Expression Atlas: ENSG00000113300 | ||
The Human Protein Atlas: ENSG00000113300 | ||
Pathway | NCI Pathway Interaction Database: CNOT6 | |
KEGG: CNOT6 | ||
REACTOME: CNOT6 | ||
ConsensusPathDB | ||
Pathway Commons: CNOT6 | ||
Metabolism | MetaCyc: CNOT6 | |
HUMANCyc: CNOT6 | ||
Regulation | Ensembl's Regulation: ENSG00000113300 | |
miRBase: chr5 :179,921,416-180,005,353 | ||
TargetScan: NM_015455 | ||
cisRED: ENSG00000113300 | ||
Context | iHOP: CNOT6 | |
cancer metabolism search in PubMed: CNOT6 | ||
UCL Cancer Institute: CNOT6 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for CNOT6(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: CNOT6 |
Familial Cancer Database: CNOT6 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
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REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: CNOT6 |
MedGen: CNOT6 (Human Medical Genetics with Condition) | |
ClinVar: CNOT6 | |
Phenotype | MGI: CNOT6 (International Mouse Phenotyping Consortium) |
PhenomicDB: CNOT6 |
Mutations for CNOT6 |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | CNOT6 | chr5 | 179975782 | 179975802 | CNOT6 | chr5 | 179976115 | 179976135 |
ovary | CNOT6 | chr5 | 179989763 | 179989783 | CNOT6 | chr5 | 179990782 | 179990802 |
ovary | CNOT6 | chr5 | 179993304 | 179993324 | chr19 | 40897007 | 40897027 | |
pancreas | CNOT6 | chr5 | 179967099 | 179967119 | CNOT6 | chr5 | 179967152 | 179967172 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CNOT6 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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Stat. for Non-Synonymous SNVs (# total SNVs=38) | (# total SNVs=10) |
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(# total SNVs=0) | (# total SNVs=1) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr5:179980414-179980414 | p.R110* | 3 |
chr5:179992944-179992944 | p.I228I | 2 |
chr5:179994980-179994980 | p.R335Q | 2 |
chr5:179994847-179994847 | p.? | 2 |
chr5:179977077-179977077 | p.R87C | 2 |
chr5:179996148-179996148 | p.L356I | 2 |
chr5:179992865-179992865 | p.A202V | 1 |
chr5:179996326-179996326 | p.S415Y | 1 |
chr5:180001041-180001041 | p.I505I | 1 |
chr5:179994874-179994874 | p.V300L | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 |   |   | 8 |   |   | 2 |   | 3 |   | 1 | 3 | 2 |   |   |   | 7 | 5 | 1 | 5 |
# mutation | 1 |   |   | 8 |   |   | 2 |   | 3 |   | 1 | 4 | 2 |   |   |   | 7 | 5 | 1 | 5 |
nonsynonymous SNV | 1 |   |   | 5 |   |   | 1 |   | 3 |   | 1 | 2 | 1 |   |   |   | 6 | 4 | 1 | 4 |
synonymous SNV |   |   |   | 3 |   |   | 1 |   |   |   |   | 2 | 1 |   |   |   | 1 | 1 |   | 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]) |
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* 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 Position | Mutation(aa) | Unique sampleID count |
chr5:179992944 | p.I228I | 2 |
chr5:179994125 | p.M192I | 1 |
chr5:179996264 | p.D365G | 1 |
chr5:179991578 | p.Y201C | 1 |
chr5:179994129 | p.V374A | 1 |
chr5:179996326 | p.A202V | 1 |
chr5:179991675 | p.E382K | 1 |
chr5:179994143 | p.A202A | 1 |
chr5:179998330 | p.L394L | 1 |
chr5:179992836 | p.R204R | 1 |
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* 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. |
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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 CNOT6 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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AFF4,APC,C5orf24,CANX,CNOT6,DDX46,ERBB2IP, FAF2,FBXW11,IPO11,KDM3B,MAML1,MAPK9,MATR3, NSD1,RBM27,SMAD5,SRFBP1,TNPO1,WDR36,ZFP62 | ADNP,SUCO,TBC1D32,CBX5,CNOT6,DCLRE1A,FLVCR1, KDM5B,MED23,PHF6,PRPF40A,PRRC1,PTBP3,RPGRIP1L, SMARCAD1,ZBTB24,ZNF254,ZNF260,ZNF286A,ZNF28,ZNF681 |
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BCLAF1,CANX,CHD1,CLSPN,CNOT6,COL4A3BP,DDX46, DIAPH1,FAF2,FBXW11,G3BP1,KDM3B,LARP1,LMNB1, MAML1,NSD1,PHAX,PRRC1,RBM27,SFXN1,YTHDC2 | BAZ1B,CHD8,CKAP5,CNOT6,HELZ,INTS2,LRBA, PIK3R4,RAD50,RBM26,RNF20,TNKS,TOP2B,TPP2, TPR,TRIM33,UBR5,USP24,USP48,VPS13C,ZNF638 |
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* 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 |
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Pharmacological Information for CNOT6 |
There's no related Drug. |
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Cross referenced IDs for CNOT6 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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