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Gene: COPS4 |
Gene summary for COPS4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COPS4 | Gene ID | 51138 |
| Gene name | COP9 signalosome subunit 4 | |
| Gene Alias | CSN4 | |
| Cytomap | 4q21.22 | |
| Gene Type | protein-coding | GO ID | GO:0000338 | UniProtAcc | Q9BT78 |
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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 |
| 51138 | COPS4 | LZE4T | Human | Esophagus | ESCC | 8.16e-11 | 2.65e-01 | 0.0811 |
| 51138 | COPS4 | LZE5T | Human | Esophagus | ESCC | 1.10e-02 | 2.14e-01 | 0.0514 |
| 51138 | COPS4 | LZE7T | Human | Esophagus | ESCC | 2.58e-05 | 3.31e-01 | 0.0667 |
| 51138 | COPS4 | LZE8T | Human | Esophagus | ESCC | 9.48e-08 | 2.40e-01 | 0.067 |
| 51138 | COPS4 | LZE24T | Human | Esophagus | ESCC | 3.69e-06 | 1.98e-01 | 0.0596 |
| 51138 | COPS4 | LZE21T | Human | Esophagus | ESCC | 1.32e-02 | 1.24e-01 | 0.0655 |
| 51138 | COPS4 | LZE6T | Human | Esophagus | ESCC | 1.12e-05 | 2.49e-01 | 0.0845 |
| 51138 | COPS4 | P1T-E | Human | Esophagus | ESCC | 4.26e-02 | 2.40e-01 | 0.0875 |
| 51138 | COPS4 | P2T-E | Human | Esophagus | ESCC | 3.56e-29 | 5.37e-01 | 0.1177 |
| 51138 | COPS4 | P4T-E | Human | Esophagus | ESCC | 3.95e-25 | 7.03e-01 | 0.1323 |
| 51138 | COPS4 | P5T-E | Human | Esophagus | ESCC | 1.20e-04 | 1.19e-01 | 0.1327 |
| 51138 | COPS4 | P8T-E | Human | Esophagus | ESCC | 3.65e-16 | 2.28e-01 | 0.0889 |
| 51138 | COPS4 | P9T-E | Human | Esophagus | ESCC | 1.54e-13 | 2.10e-01 | 0.1131 |
| 51138 | COPS4 | P10T-E | Human | Esophagus | ESCC | 2.61e-21 | 2.80e-01 | 0.116 |
| 51138 | COPS4 | P11T-E | Human | Esophagus | ESCC | 1.35e-14 | 5.20e-01 | 0.1426 |
| 51138 | COPS4 | P12T-E | Human | Esophagus | ESCC | 2.39e-23 | 4.51e-01 | 0.1122 |
| 51138 | COPS4 | P15T-E | Human | Esophagus | ESCC | 3.41e-24 | 5.50e-01 | 0.1149 |
| 51138 | COPS4 | P16T-E | Human | Esophagus | ESCC | 1.36e-25 | 4.44e-01 | 0.1153 |
| 51138 | COPS4 | P17T-E | Human | Esophagus | ESCC | 1.57e-11 | 3.47e-01 | 0.1278 |
| 51138 | COPS4 | P19T-E | Human | Esophagus | ESCC | 2.10e-05 | 3.16e-01 | 0.1662 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:007064612 | Esophagus | ESCC | protein modification by small protein removal | 95/8552 | 157/18723 | 1.25e-04 | 8.56e-04 | 95 |
| GO:000033812 | Esophagus | ESCC | protein deneddylation | 10/8552 | 10/18723 | 3.94e-04 | 2.26e-03 | 10 |
| GO:00003382 | Oral cavity | OSCC | protein deneddylation | 10/7305 | 10/18723 | 8.14e-05 | 6.26e-04 | 10 |
| GO:00706462 | Oral cavity | OSCC | protein modification by small protein removal | 77/7305 | 157/18723 | 6.55e-03 | 2.43e-02 | 77 |
| GO:00003384 | Skin | cSCC | protein deneddylation | 10/4864 | 10/18723 | 1.39e-06 | 2.40e-05 | 10 |
| GO:00706464 | Skin | cSCC | protein modification by small protein removal | 55/4864 | 157/18723 | 7.29e-03 | 3.46e-02 | 55 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| COPS4 | insertion | Nonsense_Mutation | novel | c.529_530insCCT | p.Glu177delinsAlaTer | p.E177delinsA* | protein_coding | TCGA-A8-A07G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR | |||
| COPS4 | insertion | Nonsense_Mutation | novel | c.531_532insACTGGGCAGTTGTTCTTTTAAGATCTTTAGCTTGTGAGAT | p.Ser178ThrfsTer7 | p.S178Tfs*7 | protein_coding | TCGA-A8-A07G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR | |||
| COPS4 | SNV | Missense_Mutation | c.932N>T | p.Ser311Phe | p.S311F | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-IR-A3LI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
| COPS4 | SNV | Missense_Mutation | c.64N>A | p.Leu22Met | p.L22M | protein_coding | tolerated(0.06) | possibly_damaging(0.564) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| COPS4 | SNV | Missense_Mutation | c.505A>C | p.Asn169His | p.N169H | protein_coding | deleterious(0.01) | probably_damaging(0.963) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | ||
| COPS4 | SNV | Missense_Mutation | novel | c.185N>T | p.Ser62Leu | p.S62L | protein_coding | deleterious(0) | possibly_damaging(0.754) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| COPS4 | SNV | Missense_Mutation | rs781748264 | c.84N>T | p.Gln28His | p.Q28H | protein_coding | tolerated(0.18) | benign(0) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD | |
| COPS4 | SNV | Missense_Mutation | novel | c.986A>C | p.Glu329Ala | p.E329A | protein_coding | tolerated(0.18) | benign(0.334) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| COPS4 | SNV | Missense_Mutation | c.574N>A | p.Ala192Thr | p.A192T | protein_coding | deleterious(0) | probably_damaging(0.923) | TCGA-BG-A0VZ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | CR | ||
| COPS4 | SNV | Missense_Mutation | novel | c.98C>T | p.Ala33Val | p.A33V | protein_coding | tolerated(0.66) | benign(0) | TCGA-BK-A6W3-01 | 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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