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Gene: CNOT9 |
Gene summary for CNOT9 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CNOT9 | Gene ID | 9125 |
| Gene name | CCR4-NOT transcription complex subunit 9 | |
| Gene Alias | CAF40 | |
| Cytomap | 2q35 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q92600 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 9125 | CNOT9 | HCC1 | Human | Liver | HCC | 5.52e-03 | 3.59e+00 | 0.5336 |
| 9125 | CNOT9 | HCC2 | Human | Liver | HCC | 3.06e-13 | 3.37e+00 | 0.5341 |
| 9125 | CNOT9 | S014 | Human | Liver | HCC | 1.11e-12 | 4.53e-01 | 0.2254 |
| 9125 | CNOT9 | S015 | Human | Liver | HCC | 6.82e-14 | 5.34e-01 | 0.2375 |
| 9125 | CNOT9 | S016 | Human | Liver | HCC | 1.66e-13 | 4.69e-01 | 0.2243 |
| 9125 | CNOT9 | S027 | Human | Liver | HCC | 1.64e-13 | 9.00e-01 | 0.2446 |
| 9125 | CNOT9 | S028 | Human | Liver | HCC | 5.41e-23 | 8.12e-01 | 0.2503 |
| 9125 | CNOT9 | S029 | Human | Liver | HCC | 8.82e-20 | 8.26e-01 | 0.2581 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
| GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
| GO:190136121 | Liver | HCC | organic cyclic compound catabolic process | 325/7958 | 495/18723 | 6.52e-26 | 2.18e-23 | 325 |
| GO:001943921 | Liver | HCC | aromatic compound catabolic process | 309/7958 | 467/18723 | 1.56e-25 | 4.94e-23 | 309 |
| GO:000640121 | Liver | HCC | RNA catabolic process | 201/7958 | 278/18723 | 3.88e-24 | 1.02e-21 | 201 |
| GO:003465521 | Liver | HCC | nucleobase-containing compound catabolic process | 273/7958 | 407/18723 | 4.84e-24 | 1.23e-21 | 273 |
| GO:000640221 | Liver | HCC | mRNA catabolic process | 169/7958 | 232/18723 | 4.50e-21 | 6.96e-19 | 169 |
| GO:000641722 | Liver | HCC | regulation of translation | 287/7958 | 468/18723 | 8.79e-17 | 8.08e-15 | 287 |
| GO:003052222 | Liver | HCC | intracellular receptor signaling pathway | 171/7958 | 265/18723 | 3.00e-13 | 1.61e-11 | 171 |
| GO:004854522 | Liver | HCC | response to steroid hormone | 206/7958 | 339/18723 | 6.81e-12 | 2.92e-10 | 206 |
| GO:007138322 | Liver | HCC | cellular response to steroid hormone stimulus | 128/7958 | 204/18723 | 3.92e-09 | 1.04e-07 | 128 |
| GO:004340121 | Liver | HCC | steroid hormone mediated signaling pathway | 84/7958 | 136/18723 | 4.42e-06 | 5.62e-05 | 84 |
| GO:003051821 | Liver | HCC | intracellular steroid hormone receptor signaling pathway | 73/7958 | 116/18723 | 7.04e-06 | 8.41e-05 | 73 |
| GO:003314321 | Liver | HCC | regulation of intracellular steroid hormone receptor signaling pathway | 49/7958 | 74/18723 | 3.21e-05 | 3.26e-04 | 49 |
| GO:001810511 | Liver | HCC | peptidyl-serine phosphorylation | 169/7958 | 315/18723 | 3.86e-05 | 3.81e-04 | 169 |
| GO:003812721 | Liver | HCC | ERBB signaling pathway | 73/7958 | 121/18723 | 5.65e-05 | 5.26e-04 | 73 |
| GO:0033146 | Liver | HCC | regulation of intracellular estrogen receptor signaling pathway | 26/7958 | 35/18723 | 1.37e-04 | 1.11e-03 | 26 |
| GO:000975521 | Liver | HCC | hormone-mediated signaling pathway | 106/7958 | 190/18723 | 1.45e-04 | 1.17e-03 | 106 |
| GO:001820911 | Liver | HCC | peptidyl-serine modification | 177/7958 | 338/18723 | 1.45e-04 | 1.17e-03 | 177 |
| GO:000717321 | Liver | HCC | epidermal growth factor receptor signaling pathway | 65/7958 | 108/18723 | 1.56e-04 | 1.25e-03 | 65 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa030182 | Liver | HCC | RNA degradation | 58/4020 | 79/8465 | 2.29e-06 | 2.19e-05 | 1.22e-05 | 58 |
| hsa030183 | Liver | HCC | RNA degradation | 58/4020 | 79/8465 | 2.29e-06 | 2.19e-05 | 1.22e-05 | 58 |
| Page: 1 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| CNOT9 | SNV | Missense_Mutation | c.331N>T | p.Leu111Phe | p.L111F | Q92600 | protein_coding | deleterious(0.01) | probably_damaging(0.984) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CNOT9 | SNV | Missense_Mutation | c.251N>A | p.Ala84Glu | p.A84E | Q92600 | protein_coding | tolerated(0.18) | probably_damaging(0.993) | TCGA-D8-A1XS-01 | Breast | breast invasive carcinoma | Male | <65 | III/IV | Chemotherapy | adriamycin+cyclophosphamide | SD | |
| CNOT9 | SNV | Missense_Mutation | c.815C>T | p.Ser272Leu | p.S272L | Q92600 | protein_coding | deleterious(0) | possibly_damaging(0.904) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CNOT9 | insertion | Nonsense_Mutation | novel | c.754_755insGTGATTGTCTAATTTAAAT | p.Leu252ArgfsTer6 | p.L252Rfs*6 | Q92600 | protein_coding | TCGA-A8-A09D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | ||
| CNOT9 | SNV | Missense_Mutation | c.66N>G | p.Ile22Met | p.I22M | Q92600 | protein_coding | tolerated(0.2) | benign(0.058) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| CNOT9 | SNV | Missense_Mutation | c.311N>T | p.Pro104Leu | p.P104L | Q92600 | protein_coding | deleterious(0.01) | benign(0.385) | TCGA-A6-6137-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | fluorouracil | SD | |
| CNOT9 | SNV | Missense_Mutation | c.151N>A | p.Asp51Asn | p.D51N | Q92600 | protein_coding | tolerated(0.14) | possibly_damaging(0.6) | TCGA-AA-3489-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| CNOT9 | SNV | Missense_Mutation | novel | c.380N>A | p.Ser127Asn | p.S127N | Q92600 | protein_coding | tolerated(0.14) | benign(0.085) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CNOT9 | SNV | Missense_Mutation | novel | c.674N>G | p.Asp225Gly | p.D225G | Q92600 | protein_coding | deleterious(0.01) | possibly_damaging(0.595) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| CNOT9 | SNV | Missense_Mutation | novel | c.710N>A | p.Arg237His | p.R237H | Q92600 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-AX-A1C9-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
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