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Gene: COPS7A |
Gene summary for COPS7A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COPS7A | Gene ID | 50813 |
| Gene name | COP9 signalosome subunit 7A | |
| Gene Alias | CSN7 | |
| Cytomap | 12p13.31 | |
| Gene Type | protein-coding | GO ID | GO:0000338 | UniProtAcc | Q9UBW8 |
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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 |
| 50813 | COPS7A | P44T-E | Human | Esophagus | ESCC | 6.97e-22 | 5.89e-01 | 0.1096 |
| 50813 | COPS7A | P47T-E | Human | Esophagus | ESCC | 1.66e-37 | 6.96e-01 | 0.1067 |
| 50813 | COPS7A | P48T-E | Human | Esophagus | ESCC | 4.70e-21 | 4.21e-01 | 0.0959 |
| 50813 | COPS7A | P49T-E | Human | Esophagus | ESCC | 8.51e-19 | 1.73e+00 | 0.1768 |
| 50813 | COPS7A | P52T-E | Human | Esophagus | ESCC | 2.93e-38 | 8.52e-01 | 0.1555 |
| 50813 | COPS7A | P54T-E | Human | Esophagus | ESCC | 5.40e-33 | 8.26e-01 | 0.0975 |
| 50813 | COPS7A | P56T-E | Human | Esophagus | ESCC | 7.65e-07 | 9.60e-01 | 0.1613 |
| 50813 | COPS7A | P57T-E | Human | Esophagus | ESCC | 1.10e-26 | 5.32e-01 | 0.0926 |
| 50813 | COPS7A | P61T-E | Human | Esophagus | ESCC | 2.97e-35 | 8.39e-01 | 0.099 |
| 50813 | COPS7A | P62T-E | Human | Esophagus | ESCC | 2.04e-64 | 1.08e+00 | 0.1302 |
| 50813 | COPS7A | P65T-E | Human | Esophagus | ESCC | 3.97e-27 | 5.42e-01 | 0.0978 |
| 50813 | COPS7A | P74T-E | Human | Esophagus | ESCC | 5.25e-31 | 8.85e-01 | 0.1479 |
| 50813 | COPS7A | P75T-E | Human | Esophagus | ESCC | 3.53e-29 | 5.73e-01 | 0.1125 |
| 50813 | COPS7A | P76T-E | Human | Esophagus | ESCC | 4.34e-43 | 9.18e-01 | 0.1207 |
| 50813 | COPS7A | P79T-E | Human | Esophagus | ESCC | 1.76e-33 | 6.57e-01 | 0.1154 |
| 50813 | COPS7A | P80T-E | Human | Esophagus | ESCC | 5.87e-58 | 1.50e+00 | 0.155 |
| 50813 | COPS7A | P82T-E | Human | Esophagus | ESCC | 1.98e-33 | 1.29e+00 | 0.1072 |
| 50813 | COPS7A | P83T-E | Human | Esophagus | ESCC | 2.92e-79 | 2.24e+00 | 0.1738 |
| 50813 | COPS7A | P84T-E | Human | Esophagus | ESCC | 7.99e-28 | 1.11e+00 | 0.0933 |
| 50813 | COPS7A | P89T-E | Human | Esophagus | ESCC | 1.77e-19 | 1.44e+00 | 0.1752 |
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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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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 | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:00003383 | Esophagus | HGIN | protein deneddylation | 6/2587 | 10/18723 | 8.81e-04 | 1.13e-02 | 6 |
| GO:00706463 | Esophagus | HGIN | protein modification by small protein removal | 34/2587 | 157/18723 | 4.68e-03 | 4.02e-02 | 34 |
| 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:0000338 | Liver | Cirrhotic | protein deneddylation | 7/4634 | 10/18723 | 3.29e-03 | 1.83e-02 | 7 |
| GO:00706461 | Liver | HCC | protein modification by small protein removal | 91/7958 | 157/18723 | 6.50e-05 | 5.92e-04 | 91 |
| GO:00003381 | Liver | HCC | protein deneddylation | 9/7958 | 10/18723 | 2.79e-03 | 1.31e-02 | 9 |
| 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:000033811 | Oral cavity | LP | protein deneddylation | 9/4623 | 10/18723 | 2.64e-05 | 4.21e-04 | 9 |
| 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 |
| GO:00706465 | Thyroid | PTC | protein modification by small protein removal | 71/5968 | 157/18723 | 3.03e-04 | 2.12e-03 | 71 |
| GO:007064613 | Thyroid | ATC | protein modification by small protein removal | 71/6293 | 157/18723 | 1.59e-03 | 7.99e-03 | 71 |
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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 |
| COPS7A | SNV | Missense_Mutation | c.668N>T | p.Thr223Met | p.T223M | Q9UBW8 | protein_coding | deleterious(0.01) | possibly_damaging(0.655) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| COPS7A | SNV | Missense_Mutation | rs770890062 | c.490N>T | p.Arg164Cys | p.R164C | Q9UBW8 | protein_coding | deleterious(0.01) | possibly_damaging(0.731) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| COPS7A | SNV | Missense_Mutation | c.656N>T | p.Thr219Ile | p.T219I | Q9UBW8 | protein_coding | deleterious(0.03) | benign(0.36) | TCGA-G4-6304-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | PD | |
| COPS7A | SNV | Missense_Mutation | c.754C>T | p.Arg252Cys | p.R252C | Q9UBW8 | protein_coding | deleterious(0.01) | possibly_damaging(0.719) | TCGA-AG-A014-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| COPS7A | deletion | Frame_Shift_Del | c.649delN | p.Thr219ProfsTer21 | p.T219Pfs*21 | Q9UBW8 | protein_coding | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |||
| COPS7A | deletion | Frame_Shift_Del | c.649delN | p.Thr219ProfsTer21 | p.T219Pfs*21 | Q9UBW8 | protein_coding | TCGA-AA-3815-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| COPS7A | insertion | In_Frame_Ins | novel | c.426_427insAGTAGAGAA | p.Arg142_Gly143insSerArgGlu | p.R142_G143insSRE | Q9UBW8 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| COPS7A | SNV | Missense_Mutation | novel | c.137T>G | p.Leu46Arg | p.L46R | Q9UBW8 | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| COPS7A | SNV | Missense_Mutation | novel | c.295N>A | p.Leu99Ile | p.L99I | Q9UBW8 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AJ-A23O-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| COPS7A | SNV | Missense_Mutation | novel | c.376C>T | p.Arg126Trp | p.R126W | Q9UBW8 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AJ-A3OK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | CR |
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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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