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Gene: COL7A1 |
Gene summary for COL7A1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COL7A1 | Gene ID | 1294 |
| Gene name | collagen type VII alpha 1 chain | |
| Gene Alias | EBD1 | |
| Cytomap | 3p21.31 | |
| Gene Type | protein-coding | GO ID | GO:0001704 | UniProtAcc | Q02388 |
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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 |
| 1294 | COL7A1 | CA_HPV_3 | Human | Cervix | CC | 1.42e-11 | 2.51e-01 | 0.0414 |
| 1294 | COL7A1 | CCII_1 | Human | Cervix | CC | 5.57e-60 | 1.88e+00 | 0.3249 |
| 1294 | COL7A1 | Tumor | Human | Cervix | CC | 5.78e-19 | 4.25e-01 | 0.1241 |
| 1294 | COL7A1 | sample1 | Human | Cervix | CC | 1.46e-04 | 5.31e-01 | 0.0959 |
| 1294 | COL7A1 | sample3 | Human | Cervix | CC | 2.91e-26 | 4.56e-01 | 0.1387 |
| 1294 | COL7A1 | T1 | Human | Cervix | CC | 1.19e-30 | 9.10e-01 | 0.0918 |
| 1294 | COL7A1 | T3 | Human | Cervix | CC | 1.85e-26 | 4.91e-01 | 0.1389 |
| 1294 | COL7A1 | LZE4T | Human | Esophagus | ESCC | 7.64e-07 | 2.73e-01 | 0.0811 |
| 1294 | COL7A1 | LZE7T | Human | Esophagus | ESCC | 1.05e-06 | 4.73e-01 | 0.0667 |
| 1294 | COL7A1 | LZE20T | Human | Esophagus | ESCC | 3.07e-05 | -1.81e-01 | 0.0662 |
| 1294 | COL7A1 | LZE24T | Human | Esophagus | ESCC | 8.45e-05 | 9.59e-02 | 0.0596 |
| 1294 | COL7A1 | LZE21T | Human | Esophagus | ESCC | 2.96e-02 | 5.34e-01 | 0.0655 |
| 1294 | COL7A1 | P2T-E | Human | Esophagus | ESCC | 2.75e-22 | 3.19e-01 | 0.1177 |
| 1294 | COL7A1 | P4T-E | Human | Esophagus | ESCC | 3.65e-07 | 3.55e-01 | 0.1323 |
| 1294 | COL7A1 | P5T-E | Human | Esophagus | ESCC | 2.04e-11 | -4.31e-03 | 0.1327 |
| 1294 | COL7A1 | P8T-E | Human | Esophagus | ESCC | 5.80e-04 | -7.18e-02 | 0.0889 |
| 1294 | COL7A1 | P9T-E | Human | Esophagus | ESCC | 3.45e-13 | 5.69e-01 | 0.1131 |
| 1294 | COL7A1 | P10T-E | Human | Esophagus | ESCC | 9.94e-50 | 1.32e+00 | 0.116 |
| 1294 | COL7A1 | P11T-E | Human | Esophagus | ESCC | 2.43e-17 | 1.44e+00 | 0.1426 |
| 1294 | COL7A1 | P12T-E | Human | Esophagus | ESCC | 1.37e-19 | 5.73e-01 | 0.1122 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| 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:005254710 | Cervix | CC | regulation of peptidase activity | 112/2311 | 461/18723 | 6.70e-13 | 3.08e-10 | 112 |
| GO:005254810 | Cervix | CC | regulation of endopeptidase activity | 103/2311 | 432/18723 | 1.89e-11 | 5.14e-09 | 103 |
| GO:00085446 | Cervix | CC | epidermis development | 83/2311 | 324/18723 | 3.91e-11 | 8.54e-09 | 83 |
| GO:004586110 | Cervix | CC | negative regulation of proteolysis | 80/2311 | 351/18723 | 2.88e-08 | 1.98e-06 | 80 |
| GO:00513469 | Cervix | CC | negative regulation of hydrolase activity | 81/2311 | 379/18723 | 4.27e-07 | 1.67e-05 | 81 |
| GO:00104669 | Cervix | CC | negative regulation of peptidase activity | 60/2311 | 262/18723 | 1.27e-06 | 4.34e-05 | 60 |
| GO:001095110 | Cervix | CC | negative regulation of endopeptidase activity | 56/2311 | 252/18723 | 7.43e-06 | 1.74e-04 | 56 |
| GO:00073695 | Cervix | CC | gastrulation | 42/2311 | 185/18723 | 5.83e-05 | 8.46e-04 | 42 |
| GO:00074923 | Cervix | CC | endoderm development | 20/2311 | 77/18723 | 8.40e-04 | 7.30e-03 | 20 |
| GO:0001704 | Cervix | CC | formation of primary germ layer | 27/2311 | 121/18723 | 1.49e-03 | 1.16e-02 | 27 |
| GO:0052547111 | Esophagus | ESCC | regulation of peptidase activity | 275/8552 | 461/18723 | 7.54e-10 | 1.88e-08 | 275 |
| GO:0052548111 | Esophagus | ESCC | regulation of endopeptidase activity | 253/8552 | 432/18723 | 3.68e-08 | 6.78e-07 | 253 |
| GO:000854410 | Esophagus | ESCC | epidermis development | 193/8552 | 324/18723 | 2.87e-07 | 4.19e-06 | 193 |
| GO:00073698 | Esophagus | ESCC | gastrulation | 115/8552 | 185/18723 | 4.35e-06 | 4.64e-05 | 115 |
| GO:00074926 | Esophagus | ESCC | endoderm development | 54/8552 | 77/18723 | 1.20e-05 | 1.12e-04 | 54 |
| GO:0045861111 | Esophagus | ESCC | negative regulation of proteolysis | 195/8552 | 351/18723 | 1.13e-04 | 7.85e-04 | 195 |
| GO:0051346110 | Esophagus | ESCC | negative regulation of hydrolase activity | 208/8552 | 379/18723 | 1.76e-04 | 1.14e-03 | 208 |
| GO:00017064 | Esophagus | ESCC | endoderm formation | 38/8552 | 54/18723 | 2.08e-04 | 1.31e-03 | 38 |
| GO:00017044 | Esophagus | ESCC | formation of primary germ layer | 75/8552 | 121/18723 | 2.17e-04 | 1.36e-03 | 75 |
| GO:00359873 | Esophagus | ESCC | endodermal cell differentiation | 32/8552 | 45/18723 | 4.87e-04 | 2.70e-03 | 32 |
| Page: 1 2 3 4 5 6 |
| 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 |
| COL7A1 | SNV | Missense_Mutation | rs751405989 | c.2221G>A | p.Asp741Asn | p.D741N | Q02388 | protein_coding | deleterious(0.02) | probably_damaging(0.946) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| COL7A1 | SNV | Missense_Mutation | c.1342N>C | p.Trp448Arg | p.W448R | Q02388 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-A2-A0T7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| COL7A1 | SNV | Missense_Mutation | c.6298N>T | p.Gly2100Cys | p.G2100C | Q02388 | protein_coding | tolerated(0.14) | probably_damaging(0.969) | TCGA-A8-A09T-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| COL7A1 | SNV | Missense_Mutation | c.7270C>T | p.Arg2424Trp | p.R2424W | Q02388 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-AN-A04D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| COL7A1 | SNV | Missense_Mutation | novel | c.2890N>T | p.Val964Leu | p.V964L | Q02388 | protein_coding | deleterious(0) | possibly_damaging(0.621) | TCGA-AO-A03L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD |
| COL7A1 | SNV | Missense_Mutation | c.8544N>T | p.Glu2848Asp | p.E2848D | Q02388 | protein_coding | tolerated(0.44) | benign(0.038) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| COL7A1 | SNV | Missense_Mutation | rs773146110 | c.8324N>T | p.Gly2775Val | p.G2775V | Q02388 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| COL7A1 | SNV | Missense_Mutation | rs773146110 | c.8324G>T | p.Gly2775Val | p.G2775V | Q02388 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AR-A0TQ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD |
| COL7A1 | SNV | Missense_Mutation | rs145343367 | c.1474N>A | p.Glu492Lys | p.E492K | Q02388 | protein_coding | deleterious(0.04) | probably_damaging(0.917) | TCGA-AR-A2LN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | letrozole | SD |
| COL7A1 | SNV | Missense_Mutation | c.6245N>A | p.Gly2082Glu | p.G2082E | Q02388 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-BH-A0AW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 |
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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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