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Gene: COPG1 |
Gene summary for COPG1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COPG1 | Gene ID | 22820 |
| Gene name | COPI coat complex subunit gamma 1 | |
| Gene Alias | COPG | |
| Cytomap | 3q21.3 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9Y678 |
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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 |
| 22820 | COPG1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 7.67e-03 | 3.82e-01 | -0.1808 |
| 22820 | COPG1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.81e-06 | 4.93e-01 | -0.0811 |
| 22820 | COPG1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.04e-04 | 3.27e-01 | -0.1088 |
| 22820 | COPG1 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.12e-20 | 6.08e-01 | -0.1954 |
| 22820 | COPG1 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.52e-06 | 1.21e+00 | -0.2602 |
| 22820 | COPG1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 4.27e-02 | 6.95e-01 | -0.2196 |
| 22820 | COPG1 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.90e-02 | 3.68e-01 | -0.1526 |
| 22820 | COPG1 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.13e-17 | 6.69e-01 | -0.1464 |
| 22820 | COPG1 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.54e-09 | 4.60e-01 | -0.1001 |
| 22820 | COPG1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 9.53e-07 | 5.56e-01 | -0.059 |
| 22820 | COPG1 | HTA11_2992_2000001011 | Human | Colorectum | SER | 3.43e-03 | 3.98e-01 | -0.1706 |
| 22820 | COPG1 | HTA11_5212_2000001011 | Human | Colorectum | AD | 6.02e-04 | 4.94e-01 | -0.2061 |
| 22820 | COPG1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.14e-02 | 3.26e-01 | 0.096 |
| 22820 | COPG1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.42e-02 | 3.03e-01 | 0.0674 |
| 22820 | COPG1 | HTA11_7469_2000001011 | Human | Colorectum | AD | 2.85e-02 | 6.24e-01 | -0.0124 |
| 22820 | COPG1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.12e-10 | 5.19e-01 | 0.294 |
| 22820 | COPG1 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 9.28e-03 | 1.06e+00 | 0.3487 |
| 22820 | COPG1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.65e-03 | 3.22e-01 | 0.281 |
| 22820 | COPG1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.44e-21 | 8.82e-01 | 0.3859 |
| 22820 | COPG1 | A015-C-203 | Human | Colorectum | FAP | 9.66e-04 | -1.04e-01 | -0.1294 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
| GO:0051656 | Colorectum | AD | establishment of organelle localization | 131/3918 | 390/18723 | 3.00e-09 | 2.06e-07 | 131 |
| GO:0009306 | Colorectum | AD | protein secretion | 105/3918 | 359/18723 | 1.05e-04 | 1.57e-03 | 105 |
| GO:0035592 | Colorectum | AD | establishment of protein localization to extracellular region | 105/3918 | 360/18723 | 1.18e-04 | 1.73e-03 | 105 |
| GO:0071692 | Colorectum | AD | protein localization to extracellular region | 106/3918 | 368/18723 | 1.86e-04 | 2.49e-03 | 106 |
| GO:0006888 | Colorectum | AD | endoplasmic reticulum to Golgi vesicle-mediated transport | 44/3918 | 130/18723 | 4.13e-04 | 4.68e-03 | 44 |
| GO:0030705 | Colorectum | AD | cytoskeleton-dependent intracellular transport | 60/3918 | 195/18723 | 7.56e-04 | 7.59e-03 | 60 |
| GO:0072384 | Colorectum | AD | organelle transport along microtubule | 28/3918 | 85/18723 | 6.55e-03 | 4.07e-02 | 28 |
| GO:00516561 | Colorectum | SER | establishment of organelle localization | 100/2897 | 390/18723 | 1.11e-07 | 6.79e-06 | 100 |
| GO:00481931 | Colorectum | SER | Golgi vesicle transport | 79/2897 | 296/18723 | 4.20e-07 | 2.15e-05 | 79 |
| GO:00093061 | Colorectum | SER | protein secretion | 79/2897 | 359/18723 | 5.99e-04 | 8.19e-03 | 79 |
| GO:00355921 | Colorectum | SER | establishment of protein localization to extracellular region | 79/2897 | 360/18723 | 6.54e-04 | 8.77e-03 | 79 |
| GO:00716921 | Colorectum | SER | protein localization to extracellular region | 80/2897 | 368/18723 | 8.13e-04 | 1.01e-02 | 80 |
| GO:00068881 | Colorectum | SER | endoplasmic reticulum to Golgi vesicle-mediated transport | 34/2897 | 130/18723 | 1.13e-03 | 1.29e-02 | 34 |
| GO:00307051 | Colorectum | SER | cytoskeleton-dependent intracellular transport | 44/2897 | 195/18723 | 5.53e-03 | 4.09e-02 | 44 |
| GO:00481932 | Colorectum | MSS | Golgi vesicle transport | 101/3467 | 296/18723 | 9.09e-11 | 9.77e-09 | 101 |
| GO:00516562 | Colorectum | MSS | establishment of organelle localization | 115/3467 | 390/18723 | 7.30e-08 | 3.67e-06 | 115 |
| GO:00068882 | Colorectum | MSS | endoplasmic reticulum to Golgi vesicle-mediated transport | 44/3467 | 130/18723 | 2.17e-05 | 4.60e-04 | 44 |
| GO:00093062 | Colorectum | MSS | protein secretion | 98/3467 | 359/18723 | 2.43e-05 | 5.09e-04 | 98 |
| GO:00355922 | Colorectum | MSS | establishment of protein localization to extracellular region | 98/3467 | 360/18723 | 2.75e-05 | 5.58e-04 | 98 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 |
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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 |
| COPG1 | SNV | Missense_Mutation | novel | c.1942N>T | p.Ile648Phe | p.I648F | Q9Y678 | protein_coding | deleterious(0) | benign(0.415) | TCGA-A7-A3J0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrazole | SD |
| COPG1 | SNV | Missense_Mutation | c.1339N>A | p.Glu447Lys | p.E447K | Q9Y678 | protein_coding | deleterious(0.02) | probably_damaging(0.983) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| COPG1 | SNV | Missense_Mutation | novel | c.706N>A | p.Ala236Thr | p.A236T | Q9Y678 | protein_coding | tolerated(0.21) | benign(0.078) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| COPG1 | SNV | Missense_Mutation | novel | c.1907N>A | p.Pro636His | p.P636H | Q9Y678 | protein_coding | deleterious(0) | possibly_damaging(0.783) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| COPG1 | SNV | Missense_Mutation | novel | c.425G>C | p.Arg142Pro | p.R142P | Q9Y678 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-B6-A0X1-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| COPG1 | SNV | Missense_Mutation | rs762136146 | c.611G>A | p.Arg204His | p.R204H | Q9Y678 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-BH-A0B0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| COPG1 | SNV | Missense_Mutation | novel | c.2494N>T | p.Gly832Cys | p.G832C | Q9Y678 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A27M-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | methotrexate+5 | SD |
| COPG1 | SNV | Missense_Mutation | novel | c.510N>A | p.Ser170Arg | p.S170R | Q9Y678 | protein_coding | deleterious(0.01) | probably_damaging(0.985) | TCGA-E2-A1L6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| COPG1 | SNV | Missense_Mutation | novel | c.1582G>T | p.Ala528Ser | p.A528S | Q9Y678 | protein_coding | deleterious(0.02) | benign(0.033) | TCGA-E9-A247-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| COPG1 | insertion | Nonsense_Mutation | novel | c.2555_2556insAAATAAGACAGATATATAAATAGAGAAAATAACT | p.Thr853AsnfsTer6 | p.T853Nfs*6 | Q9Y678 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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