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Gene: COPS5 |
Gene summary for COPS5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COPS5 | Gene ID | 10987 |
| Gene name | COP9 signalosome subunit 5 | |
| Gene Alias | CSN5 | |
| Cytomap | 8q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | A0A024R7W9 |
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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 |
| 10987 | COPS5 | HTA11_2487_2000001011 | Human | Colorectum | SER | 4.07e-02 | 1.83e-01 | -0.1808 |
| 10987 | COPS5 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.53e-03 | 3.29e-01 | -0.1088 |
| 10987 | COPS5 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.96e-07 | 2.54e-01 | -0.1954 |
| 10987 | COPS5 | HTA11_866_3004761011 | Human | Colorectum | AD | 6.99e-03 | 1.79e-01 | 0.096 |
| 10987 | COPS5 | HTA11_6801_2000001011 | Human | Colorectum | SER | 9.65e-03 | 3.66e-01 | 0.0171 |
| 10987 | COPS5 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.04e-06 | 2.61e-01 | 0.294 |
| 10987 | COPS5 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.17e-02 | 5.83e-01 | 0.3487 |
| 10987 | COPS5 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.20e-13 | 4.72e-01 | 0.3859 |
| 10987 | COPS5 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.73e-02 | 1.49e-01 | 0.3005 |
| 10987 | COPS5 | LZE4T | Human | Esophagus | ESCC | 3.43e-24 | 8.28e-01 | 0.0811 |
| 10987 | COPS5 | LZE5T | Human | Esophagus | ESCC | 6.45e-03 | 3.05e-01 | 0.0514 |
| 10987 | COPS5 | LZE7T | Human | Esophagus | ESCC | 5.70e-09 | 4.03e-01 | 0.0667 |
| 10987 | COPS5 | LZE8T | Human | Esophagus | ESCC | 2.35e-17 | 6.14e-01 | 0.067 |
| 10987 | COPS5 | LZE20T | Human | Esophagus | ESCC | 1.05e-15 | 7.09e-01 | 0.0662 |
| 10987 | COPS5 | LZE22D1 | Human | Esophagus | HGIN | 3.03e-04 | 1.83e-01 | 0.0595 |
| 10987 | COPS5 | LZE22T | Human | Esophagus | ESCC | 3.21e-02 | 3.54e-01 | 0.068 |
| 10987 | COPS5 | LZE24T | Human | Esophagus | ESCC | 1.41e-35 | 1.16e+00 | 0.0596 |
| 10987 | COPS5 | LZE21T | Human | Esophagus | ESCC | 6.89e-03 | 2.47e-01 | 0.0655 |
| 10987 | COPS5 | LZE6T | Human | Esophagus | ESCC | 4.84e-10 | 4.78e-01 | 0.0845 |
| 10987 | COPS5 | P1T-E | Human | Esophagus | ESCC | 1.34e-15 | 8.50e-01 | 0.0875 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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:1990182 | Colorectum | AD | exosomal secretion | 16/3918 | 20/18723 | 2.67e-08 | 1.47e-06 | 16 |
| GO:0034976 | Colorectum | AD | response to endoplasmic reticulum stress | 90/3918 | 256/18723 | 8.48e-08 | 4.28e-06 | 90 |
| GO:0097734 | Colorectum | AD | extracellular exosome biogenesis | 16/3918 | 21/18723 | 9.02e-08 | 4.52e-06 | 16 |
| GO:0140112 | Colorectum | AD | extracellular vesicle biogenesis | 16/3918 | 23/18723 | 7.04e-07 | 2.49e-05 | 16 |
| GO:0006413 | Colorectum | AD | translational initiation | 45/3918 | 118/18723 | 1.35e-05 | 2.92e-04 | 45 |
| GO:0035966 | Colorectum | AD | response to topologically incorrect protein | 54/3918 | 159/18723 | 8.85e-05 | 1.36e-03 | 54 |
| GO:0035967 | Colorectum | AD | cellular response to topologically incorrect protein | 42/3918 | 116/18723 | 1.04e-04 | 1.56e-03 | 42 |
| GO:1905897 | Colorectum | AD | regulation of response to endoplasmic reticulum stress | 32/3918 | 82/18723 | 1.37e-04 | 1.95e-03 | 32 |
| GO:0051403 | Colorectum | AD | stress-activated MAPK cascade | 72/3918 | 239/18723 | 4.77e-04 | 5.25e-03 | 72 |
| GO:0031098 | Colorectum | AD | stress-activated protein kinase signaling cascade | 74/3918 | 247/18723 | 4.80e-04 | 5.27e-03 | 74 |
| GO:0006986 | Colorectum | AD | response to unfolded protein | 45/3918 | 137/18723 | 7.43e-04 | 7.48e-03 | 45 |
| GO:0034620 | Colorectum | AD | cellular response to unfolded protein | 33/3918 | 96/18723 | 1.53e-03 | 1.29e-02 | 33 |
| GO:0070302 | Colorectum | AD | regulation of stress-activated protein kinase signaling cascade | 58/3918 | 195/18723 | 2.21e-03 | 1.74e-02 | 58 |
| GO:0006887 | Colorectum | AD | exocytosis | 96/3918 | 352/18723 | 2.48e-03 | 1.90e-02 | 96 |
| GO:0032872 | Colorectum | AD | regulation of stress-activated MAPK cascade | 57/3918 | 192/18723 | 2.51e-03 | 1.92e-02 | 57 |
| GO:0051091 | Colorectum | AD | positive regulation of DNA-binding transcription factor activity | 73/3918 | 260/18723 | 3.52e-03 | 2.54e-02 | 73 |
| GO:00349761 | Colorectum | SER | response to endoplasmic reticulum stress | 74/2897 | 256/18723 | 3.01e-08 | 2.05e-06 | 74 |
| GO:19901821 | Colorectum | SER | exosomal secretion | 13/2897 | 20/18723 | 7.51e-07 | 3.57e-05 | 13 |
| GO:00977341 | Colorectum | SER | extracellular exosome biogenesis | 13/2897 | 21/18723 | 1.69e-06 | 7.35e-05 | 13 |
| GO:01401121 | Colorectum | SER | extracellular vesicle biogenesis | 13/2897 | 23/18723 | 7.00e-06 | 2.42e-04 | 13 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| COPS5 | insertion | Frame_Shift_Ins | novel | c.98_99insC | p.Lys33AsnfsTer15 | p.K33Nfs*15 | Q92905 | protein_coding | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| COPS5 | insertion | In_Frame_Ins | novel | c.96_97insCTTGAGCCCAGTGTCGACATGCACCTTGTTTGGGTCTTC | p.Asp32_Lys33insLeuGluProSerValAspMetHisLeuValTrpValPhe | p.D32_K33insLEPSVDMHLVWVF | Q92905 | protein_coding | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| COPS5 | SNV | Missense_Mutation | c.592N>A | p.Glu198Lys | p.E198K | Q92905 | protein_coding | tolerated(0.26) | benign(0.367) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR | |
| COPS5 | SNV | Missense_Mutation | novel | c.94N>A | p.Asp32Asn | p.D32N | Q92905 | protein_coding | tolerated(0.11) | benign(0.056) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
| COPS5 | SNV | Missense_Mutation | novel | c.715N>C | p.Glu239Gln | p.E239Q | Q92905 | protein_coding | tolerated(0.05) | benign(0.027) | TCGA-MA-AA41-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| COPS5 | SNV | Missense_Mutation | novel | c.86N>G | p.Tyr29Cys | p.Y29C | Q92905 | protein_coding | deleterious(0) | possibly_damaging(0.873) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD |
| COPS5 | SNV | Missense_Mutation | rs143525514 | c.872C>T | p.Thr291Met | p.T291M | Q92905 | protein_coding | tolerated(0.13) | benign(0.15) | TCGA-AG-3902-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| COPS5 | SNV | Missense_Mutation | c.881N>A | p.Arg294Gln | p.R294Q | Q92905 | protein_coding | tolerated(0.16) | benign(0.048) | TCGA-EI-6882-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| COPS5 | SNV | Missense_Mutation | c.804T>A | p.Asp268Glu | p.D268E | Q92905 | protein_coding | deleterious(0.02) | probably_damaging(0.976) | TCGA-A5-A0GA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | taxol | PD | |
| COPS5 | SNV | Missense_Mutation | c.34N>G | p.Thr12Ala | p.T12A | Q92905 | protein_coding | tolerated(0.19) | benign(0.006) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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