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Translation Factor: CNOT9 (NCBI Gene ID:9125) |
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 Gene Summary |
| Gene Information | Gene Name: CNOT9 | Gene ID: 9125 | Gene Symbol | CNOT9 | Gene ID | 9125 |
| Gene Name | CCR4-NOT transcription complex subunit 9 | |
| Synonyms | CAF40|CT129|RCD-1|RCD1|RQCD1 | |
| Cytomap | 2q35 | |
| Type of Gene | protein-coding | |
| Description | CCR4-NOT transcription complex subunit 9RCD1 required for cell differentiation1 homologcancer/testis antigen 129cell differentiation protein RCD1 homologcell differentiation protein RQCD1 homologprotein involved in sexual development | |
| Modification date | 20200313 | |
| UniProtAcc | Q92600 | |
| Child GO biological process term(s) under GO:0006412 |
| GO ID | GO term |
| GO:0017148 | Negative regulation of translation |
| GO:0006417 | Regulation of translation |
| GO:0006412 | Translation |
| Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | CNOT9 | GO:2000327 | positive regulation of nuclear receptor transcription coactivator activity | 18180299 |
| Inferred gene age of translation factor. |
| Gene | Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25 |
| CNOT9 | >1119.25 |
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| We searched PubMed using 'CNOT9[title] AND translation [title] AND human.' |
| Gene | Title | PMID |
| CNOT9 | . | . |
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| Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. For more annotations, please visit our ExonSkipDB. |
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| Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ENST | Exon skip start (DNA) | Exon Skip end (DNA) | ORF |
| ENST00000542068 | 219445283 | 219445463 | In-frame |
| ENST00000273064 | 219449334 | 219449444 | Frame-shift |
| ENST00000542068 | 219449334 | 219449444 | Frame-shift |
| ENST00000273064 | 219457338 | 219457430 | Frame-shift |
| ENST00000542068 | 219457338 | 219457430 | Frame-shift |
| Exon skipping position in the amino acid sequence. |
| ENST | Exon skip start (DNA) | Exon Skip end (DNA) | Len(transcript seq) | Exon skip start (mRNA) | Exon Skip end (mRNA) | Len(amino acid seq) | Exon skip start (AA) | Exon Skip end (AA) |
| Potentially (partially) lost protein functional features of UniProt. |
| UniProtAcc | Exon skip start (AA) | Exon Skip end (AA) | Function feature start (AA) | Function feature end (AA) | Functional feature type | Functional feature desc. |
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| Gene expression level across TCGA pancancer |
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| Gene expression level across GTEx pantissue |
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| Expression level of gene isoforms across TCGA pancancer |
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| Expression level of gene isoforms across GTEx pantissue |
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| Cancer(tissue) type-specific expression level of Translation factor using z-score distriution |
| Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples) |
| Cancer type | Translation factor | FC | adj.pval |
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| Translation factor expression regulation through miRNA binding |
| Cancer type | Gene | miRNA | TargetScan binding score (Context++ score percentile) | Coefficient | Pvalue |
| Translation factor expression regulation through methylation in the promoter of Translation factor |
| Cancer type | Gene | methyl group b | methyl group a | DEG pval | avg methyl in b | avg methyl in a | avg exp in b | avg exp in a |
| Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation) |
| Cancer type | Gene | methyl group b | methyl group a | DEG pval | avg methyl in b | avg methyl in a | avg exp in b | avg exp in a |
| Translation factor expression regulation through copy number variation of Translation factor |
| Cancer type | Gene | Coefficient | Pvalue |
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| Strongly correlated genes belong to cellular important gene groups with CNOT9 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green) |
| Cancer type | Gene group | Translation factor | Correlated gene | Coefficient | Pvalue |
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| Protein 3D structure Visit iCn3D. |
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| Protein-protein interaction networks * Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P)) |
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| Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P)) |
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 * Edge colors based on TCGA cancer types. |
| * Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P)) |
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| Cancer type | Translation factor | Interacting protein coding gene | FC | adj.pval |
| STAD | CNOT9 | CNOT10 | -2.1943232806481 | 0.000121572986245155 |
| KIRP | CNOT9 | CNOT6L | -3.87663737407518 | 0.000364991836249828 |
| LUAD | CNOT9 | CNOT6L | -2.1633182779043 | 0.00060389239279426 |
| KIRP | CNOT9 | CNOT2 | -1.10448855710506 | 0.00222697434946895 |
| CHOL | CNOT9 | CNOT6 | -4.83321533739418 | 0.00390625 |
| CHOL | CNOT9 | CNOT8 | -1.86479733449004 | 0.00390625 |
| HNSC | CNOT9 | RQCD1 | 1.97297540658491 | 0.00585215220849023 |
| KICH | CNOT9 | CNOT3 | -1.1461250404339 | 0.00882232189178467 |
| KICH | CNOT9 | CNOT8 | 1.5062762229379 | 0.0255050659179687 |
| KIRC | CNOT9 | CNOT10 | 1.29182504470331 | 2.23846498739956e-10 |
| THCA | CNOT9 | CNOT7 | -1.0100272557073 | 2.28966131184287e-07 |
| LIHC | CNOT9 | CNOT3 | -1.23300348731276 | 3.17814170396599e-08 |
| BRCA | CNOT9 | CNOT3 | -2.12666858749727 | 9.14937084127887e-14 |
| Protein-protein interactors with this translation factor (BIOGRID-3.4.160) |
| PPI interactors with CNOT9 |
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| Clinically associated variants from ClinVar. |
| Gene | Chr | Position | RefSeq | VarSeq | RefSeeq | VarType | Pathogenic | Disease | VarInfo |
| CNOT9 | chr2 | 219447748 | T | C | single_nucleotide_variant | Likely_pathogenic | Hepatocellular_carcinoma|Transitional_cell_carcinoma_of_the_bladder|Malignant_melanoma_of_skin|Adenocarcinoma_of_stomach|Adenocarcinoma_of_prostate | SO:0001583|missense_variant,SO:0001619|non-coding_transcript_variant | SO:0001583|missense_variant,SO:0001619|non-coding_transcript_variant |
| CNOT9 | chr2 | 219447749 | C | G | single_nucleotide_variant | Likely_pathogenic | Hepatocellular_carcinoma|Transitional_cell_carcinoma_of_the_bladder|Malignant_melanoma_of_skin|Adenocarcinoma_of_stomach|Adenocarcinoma_of_prostate | SO:0001583|missense_variant,SO:0001619|non-coding_transcript_variant | SO:0001583|missense_variant,SO:0001619|non-coding_transcript_variant |
| CNOT9 | chr2 | 219449405 | C | T | single_nucleotide_variant | Likely_pathogenic | Malignant_melanoma_of_skin | SO:0001583|missense_variant | SO:0001583|missense_variant |
| CNOT9 | chr2 | 219449406 | C | T | single_nucleotide_variant | Likely_pathogenic | Malignant_melanoma_of_skin | SO:0001583|missense_variant | SO:0001583|missense_variant |
| nsSNVs with sample frequency (size of circle) from TCGA 33 cancers. |
| SNVs and Indels |
| Gene | Cancer type | Chromosome | Start | End | RefSeeq | MutSeq | Mutation type | AAchange | # samples |
| Copy number variation (CNV) of CNOT9 * Click on the image to open the original image in a new window. |
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| Fusion gene breakpoints (product of the structural variants (SVs)) across CNOT9 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion genes with this translation factor from FusionGDB2.0. |
| FusionGDB2 ID | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
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| Kaplan-Meier plots with logrank tests of overall survival (OS) |
| Cancer type | Translation factor | Coefficent | Hazard ratio | Wald test pval | Likelihool ratio pval | Logrank test pval | # samples |
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| Differential gene expression between female and male. (Wilcoxon test, pval<0.05) |
| Cancer type | Translation factor | pval | adj.p |
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| Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05) |
| Cancer type | Translation factor | pval | adj.p |
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| Drugs targeting genes involved in this translation factor. (DrugBank Version 5.1.8 2021-05-08) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| Diseases associated with this translation factor. (DisGeNet 4.0) |
| Disease ID | Disease Name | # PubMeds | Disease source |
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