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Gene: CNOT1 |
Gene summary for CNOT1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | CNOT1 | Gene ID | 23019 |
Gene name | CCR4-NOT transcription complex subunit 1 | |
Gene Alias | AD-005 | |
Cytomap | 16q21 | |
Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | A5YKK6 |
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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 |
23019 | CNOT1 | C51 | Human | Oral cavity | OSCC | 1.69e-11 | 8.68e-01 | 0.2674 |
23019 | CNOT1 | C57 | Human | Oral cavity | OSCC | 4.17e-20 | 6.53e-01 | 0.1679 |
23019 | CNOT1 | C07 | Human | Oral cavity | OSCC | 5.57e-03 | 8.53e-01 | 0.2491 |
23019 | CNOT1 | C08 | Human | Oral cavity | OSCC | 9.53e-16 | 3.66e-01 | 0.1919 |
23019 | CNOT1 | C09 | Human | Oral cavity | OSCC | 4.63e-03 | 2.52e-01 | 0.1431 |
23019 | CNOT1 | LN22 | Human | Oral cavity | OSCC | 6.37e-07 | 1.16e+00 | 0.1733 |
23019 | CNOT1 | LN46 | Human | Oral cavity | OSCC | 7.06e-08 | 6.58e-01 | 0.1666 |
23019 | CNOT1 | LP17 | Human | Oral cavity | LP | 1.46e-02 | 6.40e-01 | 0.2349 |
23019 | CNOT1 | EOLP-1 | Human | Oral cavity | EOLP | 1.65e-02 | 1.93e-01 | -0.0202 |
23019 | CNOT1 | SYSMH1 | Human | Oral cavity | OSCC | 4.68e-06 | 2.65e-01 | 0.1127 |
23019 | CNOT1 | SYSMH2 | Human | Oral cavity | OSCC | 1.69e-05 | 3.35e-01 | 0.2326 |
23019 | CNOT1 | SYSMH3 | Human | Oral cavity | OSCC | 7.17e-19 | 6.93e-01 | 0.2442 |
23019 | CNOT1 | SYSMH5 | Human | Oral cavity | OSCC | 3.85e-04 | 3.28e-01 | 0.0647 |
23019 | CNOT1 | HTA12-26-1 | Human | Pancreas | PDAC | 2.70e-07 | 5.92e-01 | 0.3728 |
23019 | CNOT1 | HTA12-29-1 | Human | Pancreas | PDAC | 9.93e-19 | 5.53e-01 | 0.3722 |
23019 | CNOT1 | 047563_1562-all-cells | Human | Prostate | BPH | 2.43e-03 | 1.83e-01 | 0.0791 |
23019 | CNOT1 | 048752_1579-all-cells | Human | Prostate | BPH | 1.01e-07 | 3.30e-01 | 0.1008 |
23019 | CNOT1 | 052095_1628-all-cells | Human | Prostate | BPH | 6.25e-11 | 3.86e-01 | 0.1032 |
23019 | CNOT1 | 052097_1595-all-cells | Human | Prostate | BPH | 9.07e-10 | 4.25e-01 | 0.0972 |
23019 | CNOT1 | 052099_1652-all-cells | Human | Prostate | BPH | 2.36e-04 | 3.05e-01 | 0.1038 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000989610 | Cervix | CC | positive regulation of catabolic process | 109/2311 | 492/18723 | 5.26e-10 | 6.99e-08 | 109 |
GO:003133110 | Cervix | CC | positive regulation of cellular catabolic process | 91/2311 | 427/18723 | 9.64e-08 | 5.25e-06 | 91 |
GO:00064029 | Cervix | CC | mRNA catabolic process | 56/2311 | 232/18723 | 4.81e-07 | 1.83e-05 | 56 |
GO:004854510 | Cervix | CC | response to steroid hormone | 74/2311 | 339/18723 | 5.71e-07 | 2.09e-05 | 74 |
GO:19001517 | Cervix | CC | regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 11/2311 | 18/18723 | 1.37e-06 | 4.55e-05 | 11 |
GO:19033119 | Cervix | CC | regulation of mRNA metabolic process | 64/2311 | 288/18723 | 1.71e-06 | 5.64e-05 | 64 |
GO:00305229 | Cervix | CC | intracellular receptor signaling pathway | 60/2311 | 265/18723 | 1.89e-06 | 5.97e-05 | 60 |
GO:00064019 | Cervix | CC | RNA catabolic process | 62/2311 | 278/18723 | 2.18e-06 | 6.56e-05 | 62 |
GO:00002896 | Cervix | CC | nuclear-transcribed mRNA poly(A) tail shortening | 13/2311 | 29/18723 | 1.48e-05 | 2.93e-04 | 13 |
GO:00602119 | Cervix | CC | regulation of nuclear-transcribed mRNA poly(A) tail shortening | 9/2311 | 15/18723 | 1.63e-05 | 3.17e-04 | 9 |
GO:19001536 | Cervix | CC | positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 9/2311 | 15/18723 | 1.63e-05 | 3.17e-04 | 9 |
GO:000641710 | Cervix | CC | regulation of translation | 89/2311 | 468/18723 | 1.86e-05 | 3.46e-04 | 89 |
GO:00009567 | Cervix | CC | nuclear-transcribed mRNA catabolic process | 30/2311 | 112/18723 | 2.60e-05 | 4.37e-04 | 30 |
GO:00602139 | Cervix | CC | positive regulation of nuclear-transcribed mRNA poly(A) tail shortening | 8/2311 | 13/18723 | 3.85e-05 | 6.05e-04 | 8 |
GO:00017018 | Cervix | CC | in utero embryonic development | 71/2311 | 367/18723 | 7.21e-05 | 1.00e-03 | 71 |
GO:00002886 | Cervix | CC | nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 18/2311 | 56/18723 | 8.42e-05 | 1.13e-03 | 18 |
GO:00610139 | Cervix | CC | regulation of mRNA catabolic process | 38/2311 | 166/18723 | 1.07e-04 | 1.36e-03 | 38 |
GO:19033136 | Cervix | CC | positive regulation of mRNA metabolic process | 29/2311 | 118/18723 | 1.86e-04 | 2.18e-03 | 29 |
GO:19021153 | Cervix | CC | regulation of organelle assembly | 40/2311 | 186/18723 | 2.92e-04 | 3.15e-03 | 40 |
GO:00467008 | Cervix | CC | heterocycle catabolic process | 80/2311 | 445/18723 | 3.23e-04 | 3.42e-03 | 80 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa030187 | Endometrium | EEC | RNA degradation | 20/1237 | 79/8465 | 8.36e-03 | 3.88e-02 | 2.89e-02 | 20 |
hsa0301812 | Endometrium | EEC | RNA degradation | 20/1237 | 79/8465 | 8.36e-03 | 3.88e-02 | 2.89e-02 | 20 |
hsa0301810 | Esophagus | HGIN | RNA degradation | 27/1383 | 79/8465 | 7.73e-05 | 9.00e-04 | 7.15e-04 | 27 |
hsa0301815 | Esophagus | HGIN | RNA degradation | 27/1383 | 79/8465 | 7.73e-05 | 9.00e-04 | 7.15e-04 | 27 |
hsa0301824 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
hsa0301834 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
hsa03018 | Liver | Cirrhotic | RNA degradation | 44/2530 | 79/8465 | 1.43e-06 | 1.65e-05 | 1.02e-05 | 44 |
hsa030181 | Liver | Cirrhotic | RNA degradation | 44/2530 | 79/8465 | 1.43e-06 | 1.65e-05 | 1.02e-05 | 44 |
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 |
hsa030189 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
hsa0301814 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
hsa0301823 | Oral cavity | LP | RNA degradation | 39/2418 | 79/8465 | 6.98e-05 | 4.38e-04 | 2.83e-04 | 39 |
hsa0301833 | Oral cavity | LP | RNA degradation | 39/2418 | 79/8465 | 6.98e-05 | 4.38e-04 | 2.83e-04 | 39 |
hsa0301841 | Oral cavity | EOLP | RNA degradation | 22/1218 | 79/8465 | 1.33e-03 | 4.80e-03 | 2.83e-03 | 22 |
hsa0301851 | Oral cavity | EOLP | RNA degradation | 22/1218 | 79/8465 | 1.33e-03 | 4.80e-03 | 2.83e-03 | 22 |
hsa030188 | Prostate | BPH | RNA degradation | 29/1718 | 79/8465 | 5.17e-04 | 2.67e-03 | 1.65e-03 | 29 |
hsa0301813 | Prostate | BPH | RNA degradation | 29/1718 | 79/8465 | 5.17e-04 | 2.67e-03 | 1.65e-03 | 29 |
hsa0301822 | Prostate | Tumor | RNA degradation | 30/1791 | 79/8465 | 4.48e-04 | 2.35e-03 | 1.46e-03 | 30 |
hsa0301832 | Prostate | Tumor | RNA degradation | 30/1791 | 79/8465 | 4.48e-04 | 2.35e-03 | 1.46e-03 | 30 |
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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 |
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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. |
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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 |
CNOT1 | SNV | Missense_Mutation | c.6685C>A | p.His2229Asn | p.H2229N | A5YKK6 | protein_coding | tolerated(0.15) | benign(0.062) | TCGA-A8-A09A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
CNOT1 | SNV | Missense_Mutation | c.811N>C | p.Glu271Gln | p.E271Q | A5YKK6 | protein_coding | tolerated(0.05) | benign(0.08) | TCGA-AN-A0FV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
CNOT1 | SNV | Missense_Mutation | novel | c.5214N>A | p.Asn1738Lys | p.N1738K | A5YKK6 | protein_coding | deleterious(0.02) | benign(0.392) | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CNOT1 | SNV | Missense_Mutation | novel | c.2692N>A | p.Glu898Lys | p.E898K | A5YKK6 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AR-A2LE-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | PD |
CNOT1 | SNV | Missense_Mutation | c.3662T>C | p.Leu1221Pro | p.L1221P | A5YKK6 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
CNOT1 | SNV | Missense_Mutation | c.2545N>T | p.Asn849Tyr | p.N849Y | A5YKK6 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-BH-A1F5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
CNOT1 | SNV | Missense_Mutation | c.5563N>G | p.Leu1855Val | p.L1855V | A5YKK6 | protein_coding | deleterious(0) | benign(0.184) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
CNOT1 | SNV | Missense_Mutation | c.4606N>A | p.Glu1536Lys | p.E1536K | A5YKK6 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
CNOT1 | SNV | Missense_Mutation | c.2891G>A | p.Arg964Lys | p.R964K | A5YKK6 | protein_coding | tolerated(0.44) | benign(0.152) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
CNOT1 | SNV | Missense_Mutation | c.3023N>G | p.Ser1008Cys | p.S1008C | A5YKK6 | protein_coding | deleterious(0.04) | possibly_damaging(0.527) | TCGA-LL-A73Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | 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 |
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