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Gene: COPE |
Gene summary for COPE |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COPE | Gene ID | 11316 |
| Gene name | COPI coat complex subunit epsilon | |
| Gene Alias | epsilon-COP | |
| Cytomap | 19p13.11 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | M0QXB4 |
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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 |
| 11316 | COPE | GSM4909282 | Human | Breast | IDC | 4.40e-02 | 2.58e-01 | -0.0288 |
| 11316 | COPE | GSM4909285 | Human | Breast | IDC | 3.09e-34 | 7.21e-01 | 0.21 |
| 11316 | COPE | GSM4909286 | Human | Breast | IDC | 4.21e-13 | -3.25e-01 | 0.1081 |
| 11316 | COPE | GSM4909287 | Human | Breast | IDC | 5.79e-12 | 4.64e-01 | 0.2057 |
| 11316 | COPE | GSM4909290 | Human | Breast | IDC | 1.89e-03 | 3.84e-01 | 0.2096 |
| 11316 | COPE | GSM4909291 | Human | Breast | IDC | 2.13e-08 | 4.84e-01 | 0.1753 |
| 11316 | COPE | GSM4909294 | Human | Breast | IDC | 4.92e-06 | 1.05e-01 | 0.2022 |
| 11316 | COPE | GSM4909296 | Human | Breast | IDC | 1.14e-12 | 1.85e-01 | 0.1524 |
| 11316 | COPE | GSM4909297 | Human | Breast | IDC | 2.64e-16 | -1.10e-01 | 0.1517 |
| 11316 | COPE | GSM4909304 | Human | Breast | IDC | 1.42e-06 | 3.74e-01 | 0.1636 |
| 11316 | COPE | GSM4909308 | Human | Breast | IDC | 1.72e-09 | 4.54e-01 | 0.158 |
| 11316 | COPE | GSM4909311 | Human | Breast | IDC | 9.57e-40 | -2.72e-01 | 0.1534 |
| 11316 | COPE | GSM4909312 | Human | Breast | IDC | 1.94e-13 | -4.87e-02 | 0.1552 |
| 11316 | COPE | GSM4909316 | Human | Breast | IDC | 1.86e-11 | 4.66e-01 | 0.21 |
| 11316 | COPE | GSM4909319 | Human | Breast | IDC | 8.11e-54 | -1.16e-01 | 0.1563 |
| 11316 | COPE | GSM4909320 | Human | Breast | IDC | 7.47e-04 | -1.01e-01 | 0.1575 |
| 11316 | COPE | GSM4909321 | Human | Breast | IDC | 1.06e-19 | -6.14e-02 | 0.1559 |
| 11316 | COPE | brca1 | Human | Breast | Precancer | 1.10e-15 | 4.76e-01 | -0.0338 |
| 11316 | COPE | brca2 | Human | Breast | Precancer | 7.06e-14 | 4.64e-01 | -0.024 |
| 11316 | COPE | brca3 | Human | Breast | Precancer | 5.48e-10 | 4.40e-01 | -0.0263 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:00068906 | Breast | IDC | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 10/1434 | 52/18723 | 5.49e-03 | 4.03e-02 | 10 |
| GO:000689012 | Breast | DCIS | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 10/1390 | 52/18723 | 4.41e-03 | 3.41e-02 | 10 |
| GO:00481938 | Cervix | CC | Golgi vesicle transport | 58/2311 | 296/18723 | 2.24e-04 | 2.54e-03 | 58 |
| GO:00068907 | Cervix | CC | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 15/2311 | 52/18723 | 1.15e-03 | 9.39e-03 | 15 |
| GO:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
| GO:0006890 | Colorectum | AD | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 27/3918 | 52/18723 | 7.67e-07 | 2.70e-05 | 27 |
| GO:0006888 | Colorectum | AD | endoplasmic reticulum to Golgi vesicle-mediated transport | 44/3918 | 130/18723 | 4.13e-04 | 4.68e-03 | 44 |
| GO:00481931 | Colorectum | SER | Golgi vesicle transport | 79/2897 | 296/18723 | 4.20e-07 | 2.15e-05 | 79 |
| GO:00068901 | Colorectum | SER | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 20/2897 | 52/18723 | 4.80e-05 | 1.18e-03 | 20 |
| GO:00068881 | Colorectum | SER | endoplasmic reticulum to Golgi vesicle-mediated transport | 34/2897 | 130/18723 | 1.13e-03 | 1.29e-02 | 34 |
| GO:00481932 | Colorectum | MSS | Golgi vesicle transport | 101/3467 | 296/18723 | 9.09e-11 | 9.77e-09 | 101 |
| 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:00068903 | Colorectum | MSI-H | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 13/1319 | 52/18723 | 4.72e-05 | 1.69e-03 | 13 |
| GO:00068883 | Colorectum | MSI-H | endoplasmic reticulum to Golgi vesicle-mediated transport | 22/1319 | 130/18723 | 1.05e-04 | 3.24e-03 | 22 |
| GO:00481933 | Colorectum | MSI-H | Golgi vesicle transport | 39/1319 | 296/18723 | 1.17e-04 | 3.51e-03 | 39 |
| GO:00481939 | Endometrium | AEH | Golgi vesicle transport | 60/2100 | 296/18723 | 3.65e-06 | 9.79e-05 | 60 |
| GO:00068886 | Endometrium | AEH | endoplasmic reticulum to Golgi vesicle-mediated transport | 29/2100 | 130/18723 | 2.11e-04 | 2.59e-03 | 29 |
| GO:00068908 | Endometrium | AEH | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 15/2100 | 52/18723 | 4.20e-04 | 4.46e-03 | 15 |
| GO:004819313 | Endometrium | EEC | Golgi vesicle transport | 60/2168 | 296/18723 | 9.91e-06 | 2.17e-04 | 60 |
| Page: 1 2 3 4 |
| 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 |
| COPE | SNV | Missense_Mutation | c.41N>C | p.Gly14Ala | p.G14A | protein_coding | tolerated(0.09) | probably_damaging(0.998) | TCGA-A1-A0SK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| COPE | SNV | Missense_Mutation | novel | c.269N>C | p.Tyr90Ser | p.Y90S | protein_coding | deleterious(0) | benign(0.287) | TCGA-AN-A0FL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| COPE | deletion | Frame_Shift_Del | novel | c.919delN | p.His307IlefsTer35 | p.H307Ifs*35 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
| COPE | insertion | Frame_Shift_Ins | novel | c.956dupA | p.Asp319GlufsTer3 | p.D319Efs*3 | protein_coding | TCGA-GM-A2DH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | CR | |||
| COPE | SNV | Missense_Mutation | rs770712891 | c.511N>T | p.Arg171Cys | p.R171C | protein_coding | tolerated_low_confidence(0.12) | benign(0.043) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| COPE | SNV | Missense_Mutation | c.282G>T | p.Glu94Asp | p.E94D | protein_coding | tolerated(0.57) | benign(0.012) | TCGA-C5-A3HE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | ||
| COPE | SNV | Missense_Mutation | novel | c.781C>A | p.Leu261Met | p.L261M | protein_coding | tolerated(0.15) | possibly_damaging(0.642) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| COPE | SNV | Missense_Mutation | c.205N>A | p.Val69Ile | p.V69I | protein_coding | deleterious(0.05) | possibly_damaging(0.735) | TCGA-AA-3713-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | PR | ||
| COPE | SNV | Missense_Mutation | rs751347373 | c.340G>A | p.Val114Met | p.V114M | protein_coding | tolerated(0.09) | probably_damaging(0.939) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| COPE | SNV | Missense_Mutation | rs575079459 | c.334N>A | p.Val112Met | p.V112M | protein_coding | tolerated(0.07) | benign(0.097) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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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