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Gene: COPG2 |
Gene summary for COPG2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COPG2 | Gene ID | 26958 |
| Gene name | COPI coat complex subunit gamma 2 | |
| Gene Alias | 2-COP | |
| Cytomap | 7q32.2 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9NSM7 |
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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 |
| 26958 | COPG2 | P75T-E | Human | Esophagus | ESCC | 3.37e-11 | 2.22e-01 | 0.1125 |
| 26958 | COPG2 | P79T-E | Human | Esophagus | ESCC | 8.01e-15 | 3.10e-01 | 0.1154 |
| 26958 | COPG2 | P80T-E | Human | Esophagus | ESCC | 3.02e-19 | 6.22e-01 | 0.155 |
| 26958 | COPG2 | P82T-E | Human | Esophagus | ESCC | 1.52e-05 | 2.80e-01 | 0.1072 |
| 26958 | COPG2 | P83T-E | Human | Esophagus | ESCC | 2.47e-21 | 4.31e-01 | 0.1738 |
| 26958 | COPG2 | P89T-E | Human | Esophagus | ESCC | 1.97e-07 | 4.40e-01 | 0.1752 |
| 26958 | COPG2 | P91T-E | Human | Esophagus | ESCC | 4.45e-06 | 7.58e-01 | 0.1828 |
| 26958 | COPG2 | P107T-E | Human | Esophagus | ESCC | 3.23e-10 | 1.97e-01 | 0.171 |
| 26958 | COPG2 | P126T-E | Human | Esophagus | ESCC | 9.16e-03 | 3.17e-01 | 0.1125 |
| 26958 | COPG2 | P127T-E | Human | Esophagus | ESCC | 1.03e-06 | 1.32e-01 | 0.0826 |
| 26958 | COPG2 | P128T-E | Human | Esophagus | ESCC | 1.76e-21 | 6.24e-01 | 0.1241 |
| 26958 | COPG2 | P130T-E | Human | Esophagus | ESCC | 2.25e-45 | 9.62e-01 | 0.1676 |
| 26958 | COPG2 | C04 | Human | Oral cavity | OSCC | 1.28e-05 | 3.13e-01 | 0.2633 |
| 26958 | COPG2 | C21 | Human | Oral cavity | OSCC | 3.85e-07 | 2.72e-01 | 0.2678 |
| 26958 | COPG2 | C30 | Human | Oral cavity | OSCC | 8.02e-08 | 4.47e-01 | 0.3055 |
| 26958 | COPG2 | C38 | Human | Oral cavity | OSCC | 2.49e-03 | 4.37e-01 | 0.172 |
| 26958 | COPG2 | C43 | Human | Oral cavity | OSCC | 4.23e-05 | 1.80e-01 | 0.1704 |
| 26958 | COPG2 | C46 | Human | Oral cavity | OSCC | 5.06e-08 | 2.88e-01 | 0.1673 |
| 26958 | COPG2 | C07 | Human | Oral cavity | OSCC | 2.61e-02 | 4.39e-01 | 0.2491 |
| 26958 | COPG2 | C08 | Human | Oral cavity | OSCC | 2.07e-22 | 4.56e-01 | 0.1919 |
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| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:0006890 | Colorectum | AD | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 27/3918 | 52/18723 | 7.67e-07 | 2.70e-05 | 27 |
| 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: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:00068902 | Colorectum | MSS | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 26/3467 | 52/18723 | 2.66e-07 | 1.10e-05 | 26 |
| 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 |
| GO:00716922 | Colorectum | MSS | protein localization to extracellular region | 99/3467 | 368/18723 | 4.17e-05 | 7.83e-04 | 99 |
| GO:00307052 | Colorectum | MSS | cytoskeleton-dependent intracellular transport | 52/3467 | 195/18723 | 3.07e-03 | 2.34e-02 | 52 |
| GO:00516563 | Colorectum | FAP | establishment of organelle localization | 97/2622 | 390/18723 | 5.91e-09 | 9.48e-07 | 97 |
| GO:00481934 | Colorectum | FAP | Golgi vesicle transport | 77/2622 | 296/18723 | 2.86e-08 | 2.62e-06 | 77 |
| GO:00093063 | Colorectum | FAP | protein secretion | 79/2622 | 359/18723 | 2.24e-05 | 5.31e-04 | 79 |
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| 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. |
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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 |
| COPG2 | SNV | Missense_Mutation | rs782187967 | c.290N>A | p.Thr97Asn | p.T97N | Q9UBF2 | protein_coding | tolerated(0.51) | benign(0.005) | TCGA-A2-A0D0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| COPG2 | SNV | Missense_Mutation | c.234A>C | p.Gln78His | p.Q78H | Q9UBF2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| COPG2 | SNV | Missense_Mutation | c.724N>C | p.Glu242Gln | p.E242Q | Q9UBF2 | protein_coding | deleterious(0.02) | possibly_damaging(0.644) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| COPG2 | SNV | Missense_Mutation | rs372285287 | c.2606C>A | p.Ser869Tyr | p.S869Y | Q9UBF2 | protein_coding | deleterious(0) | probably_damaging(0.956) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| COPG2 | SNV | Missense_Mutation | rs782187967 | c.290N>A | p.Thr97Asn | p.T97N | Q9UBF2 | protein_coding | tolerated(0.51) | benign(0.005) | TCGA-BH-A0BG-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| COPG2 | SNV | Missense_Mutation | rs782187967 | c.290N>A | p.Thr97Asn | p.T97N | Q9UBF2 | protein_coding | tolerated(0.51) | benign(0.005) | TCGA-C8-A12X-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| COPG2 | SNV | Missense_Mutation | novel | c.2275N>C | p.Asp759His | p.D759H | Q9UBF2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-E2-A1B1-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Other, specify in notesbiphosphonate | zoledronic | SD |
| COPG2 | SNV | Missense_Mutation | c.421N>A | p.Glu141Lys | p.E141K | Q9UBF2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-E9-A1N9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| COPG2 | insertion | Frame_Shift_Ins | novel | c.84dupA | p.Gln29ThrfsTer8 | p.Q29Tfs*8 | Q9UBF2 | protein_coding | TCGA-S3-AA11-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | letrozole | CR | ||
| COPG2 | SNV | Missense_Mutation | c.28N>A | p.Glu10Lys | p.E10K | Q9UBF2 | protein_coding | deleterious(0) | benign(0.223) | TCGA-WL-A834-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | paclitaxel | 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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