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Gene: COL4A5 |
Gene summary for COL4A5 |
Gene summary. |
Gene information | Species | Human | Gene symbol | COL4A5 | Gene ID | 1287 |
Gene name | collagen type IV alpha 5 chain | |
Gene Alias | ASLN | |
Cytomap | Xq22.3 | |
Gene Type | protein-coding | GO ID | GO:0007154 | UniProtAcc | A7MBN3 |
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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 |
1287 | COL4A5 | LZE4T | Human | Esophagus | ESCC | 1.05e-11 | 4.32e-01 | 0.0811 |
1287 | COL4A5 | LZE7T | Human | Esophagus | ESCC | 1.26e-08 | 5.22e-01 | 0.0667 |
1287 | COL4A5 | LZE8T | Human | Esophagus | ESCC | 5.82e-03 | 1.25e-01 | 0.067 |
1287 | COL4A5 | LZE22T | Human | Esophagus | ESCC | 2.43e-03 | 4.23e-01 | 0.068 |
1287 | COL4A5 | LZE24T | Human | Esophagus | ESCC | 5.37e-09 | 4.64e-01 | 0.0596 |
1287 | COL4A5 | LZE6T | Human | Esophagus | ESCC | 5.81e-04 | 3.54e-01 | 0.0845 |
1287 | COL4A5 | P1T-E | Human | Esophagus | ESCC | 2.12e-04 | 3.73e-01 | 0.0875 |
1287 | COL4A5 | P2T-E | Human | Esophagus | ESCC | 1.02e-14 | 3.51e-01 | 0.1177 |
1287 | COL4A5 | P4T-E | Human | Esophagus | ESCC | 1.12e-05 | 1.74e-01 | 0.1323 |
1287 | COL4A5 | P5T-E | Human | Esophagus | ESCC | 7.29e-11 | 1.42e-01 | 0.1327 |
1287 | COL4A5 | P8T-E | Human | Esophagus | ESCC | 6.83e-31 | 7.10e-01 | 0.0889 |
1287 | COL4A5 | P9T-E | Human | Esophagus | ESCC | 5.74e-04 | 1.40e-01 | 0.1131 |
1287 | COL4A5 | P10T-E | Human | Esophagus | ESCC | 1.97e-32 | 7.26e-01 | 0.116 |
1287 | COL4A5 | P11T-E | Human | Esophagus | ESCC | 8.02e-09 | 4.11e-01 | 0.1426 |
1287 | COL4A5 | P12T-E | Human | Esophagus | ESCC | 1.95e-23 | 4.62e-01 | 0.1122 |
1287 | COL4A5 | P15T-E | Human | Esophagus | ESCC | 1.77e-16 | 3.78e-01 | 0.1149 |
1287 | COL4A5 | P16T-E | Human | Esophagus | ESCC | 5.60e-11 | 1.25e-01 | 0.1153 |
1287 | COL4A5 | P20T-E | Human | Esophagus | ESCC | 4.50e-29 | 6.89e-01 | 0.1124 |
1287 | COL4A5 | P21T-E | Human | Esophagus | ESCC | 1.71e-13 | 1.93e-01 | 0.1617 |
1287 | COL4A5 | P22T-E | Human | Esophagus | ESCC | 2.78e-11 | 2.82e-01 | 0.1236 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00301984 | Esophagus | ESCC | extracellular matrix organization | 171/8552 | 301/18723 | 6.08e-05 | 4.67e-04 | 171 |
GO:00430624 | Esophagus | ESCC | extracellular structure organization | 171/8552 | 302/18723 | 7.73e-05 | 5.76e-04 | 171 |
GO:00452294 | Esophagus | ESCC | external encapsulating structure organization | 172/8552 | 304/18723 | 7.80e-05 | 5.80e-04 | 172 |
GO:005080811 | Lung | AIS | synapse organization | 63/1849 | 426/18723 | 7.39e-04 | 1.07e-02 | 63 |
GO:00301983 | Oral cavity | OSCC | extracellular matrix organization | 146/7305 | 301/18723 | 4.67e-04 | 2.77e-03 | 146 |
GO:00452293 | Oral cavity | OSCC | external encapsulating structure organization | 147/7305 | 304/18723 | 5.30e-04 | 3.08e-03 | 147 |
GO:00430623 | Oral cavity | OSCC | extracellular structure organization | 146/7305 | 302/18723 | 5.59e-04 | 3.23e-03 | 146 |
GO:00301982 | Oral cavity | NEOLP | extracellular matrix organization | 64/2005 | 301/18723 | 5.66e-08 | 2.24e-06 | 64 |
GO:00430622 | Oral cavity | NEOLP | extracellular structure organization | 64/2005 | 302/18723 | 6.44e-08 | 2.50e-06 | 64 |
GO:00452292 | Oral cavity | NEOLP | external encapsulating structure organization | 64/2005 | 304/18723 | 8.33e-08 | 3.17e-06 | 64 |
GO:00508087 | Prostate | BPH | synapse organization | 103/3107 | 426/18723 | 3.19e-05 | 3.61e-04 | 103 |
GO:00430621 | Prostate | BPH | extracellular structure organization | 67/3107 | 302/18723 | 6.67e-03 | 3.00e-02 | 67 |
GO:0038063 | Prostate | BPH | collagen-activated tyrosine kinase receptor signaling pathway | 6/3107 | 12/18723 | 7.73e-03 | 3.39e-02 | 6 |
GO:00301981 | Prostate | BPH | extracellular matrix organization | 66/3107 | 301/18723 | 9.20e-03 | 3.92e-02 | 66 |
GO:00452291 | Prostate | BPH | external encapsulating structure organization | 66/3107 | 304/18723 | 1.15e-02 | 4.66e-02 | 66 |
GO:005080813 | Prostate | Tumor | synapse organization | 105/3246 | 426/18723 | 7.20e-05 | 7.62e-04 | 105 |
GO:00508088 | Skin | AK | synapse organization | 71/1910 | 426/18723 | 2.21e-05 | 4.07e-04 | 71 |
GO:005080814 | Skin | SCCIS | synapse organization | 42/919 | 426/18723 | 1.43e-05 | 4.70e-04 | 42 |
GO:00301985 | Skin | SCCIS | extracellular matrix organization | 32/919 | 301/18723 | 3.46e-05 | 9.17e-04 | 32 |
GO:00430625 | Skin | SCCIS | extracellular structure organization | 32/919 | 302/18723 | 3.69e-05 | 9.65e-04 | 32 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa052229 | Esophagus | ESCC | Small cell lung cancer | 69/4205 | 92/8465 | 5.40e-07 | 3.85e-06 | 1.97e-06 | 69 |
hsa0493310 | Esophagus | ESCC | AGE-RAGE signaling pathway in diabetic complications | 72/4205 | 100/8465 | 4.15e-06 | 2.28e-05 | 1.17e-05 | 72 |
hsa0451020 | Esophagus | ESCC | Focal adhesion | 127/4205 | 203/8465 | 1.25e-04 | 4.99e-04 | 2.56e-04 | 127 |
hsa049268 | Esophagus | ESCC | Relaxin signaling pathway | 81/4205 | 129/8465 | 1.72e-03 | 5.09e-03 | 2.61e-03 | 81 |
hsa041517 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
hsa0516515 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa0522216 | Esophagus | ESCC | Small cell lung cancer | 69/4205 | 92/8465 | 5.40e-07 | 3.85e-06 | 1.97e-06 | 69 |
hsa0493317 | Esophagus | ESCC | AGE-RAGE signaling pathway in diabetic complications | 72/4205 | 100/8465 | 4.15e-06 | 2.28e-05 | 1.17e-05 | 72 |
hsa04510111 | Esophagus | ESCC | Focal adhesion | 127/4205 | 203/8465 | 1.25e-04 | 4.99e-04 | 2.56e-04 | 127 |
hsa0492616 | Esophagus | ESCC | Relaxin signaling pathway | 81/4205 | 129/8465 | 1.72e-03 | 5.09e-03 | 2.61e-03 | 81 |
hsa0415114 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
hsa0451022 | Lung | AIS | Focal adhesion | 57/961 | 203/8465 | 3.17e-11 | 3.43e-09 | 2.19e-09 | 57 |
hsa0516521 | Lung | AIS | Human papillomavirus infection | 64/961 | 331/8465 | 1.03e-05 | 3.04e-04 | 1.95e-04 | 64 |
hsa0522221 | Lung | AIS | Small cell lung cancer | 21/961 | 92/8465 | 1.23e-03 | 9.02e-03 | 5.77e-03 | 21 |
hsa045122 | Lung | AIS | ECM-receptor interaction | 20/961 | 89/8465 | 1.95e-03 | 1.26e-02 | 8.09e-03 | 20 |
hsa0415121 | Lung | AIS | PI3K-Akt signaling pathway | 57/961 | 354/8465 | 3.72e-03 | 2.00e-02 | 1.28e-02 | 57 |
hsa0492621 | Lung | AIS | Relaxin signaling pathway | 25/961 | 129/8465 | 4.95e-03 | 2.47e-02 | 1.58e-02 | 25 |
hsa0514621 | Lung | AIS | Amoebiasis | 20/961 | 102/8465 | 9.86e-03 | 4.20e-02 | 2.69e-02 | 20 |
hsa0451032 | Lung | AIS | Focal adhesion | 57/961 | 203/8465 | 3.17e-11 | 3.43e-09 | 2.19e-09 | 57 |
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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 |
COL4A5 | ITGA1_ITGB1 | COL4A5_ITGA1_ITGB1 | COLLAGEN | Cervix | CC |
COL4A5 | ITGA2_ITGB1 | COL4A5_ITGA2_ITGB1 | COLLAGEN | Cervix | CC |
COL4A5 | ITGA3_ITGB1 | COL4A5_ITGA3_ITGB1 | COLLAGEN | Cervix | CC |
COL4A5 | ITGA9_ITGB1 | COL4A5_ITGA9_ITGB1 | COLLAGEN | Cervix | CC |
COL4A5 | ITGA11_ITGB1 | COL4A5_ITGA11_ITGB1 | COLLAGEN | Cervix | CC |
COL4A5 | ITGAV_ITGB8 | COL4A5_ITGAV_ITGB8 | COLLAGEN | Cervix | CC |
COL4A5 | CD44 | COL4A5_CD44 | COLLAGEN | Cervix | CC |
COL4A5 | SDC1 | COL4A5_SDC1 | COLLAGEN | Cervix | CC |
COL4A5 | SDC4 | COL4A5_SDC4 | COLLAGEN | Cervix | CC |
COL4A5 | ITGA1_ITGB1 | COL4A5_ITGA1_ITGB1 | COLLAGEN | CRC | AD |
COL4A5 | ITGA2_ITGB1 | COL4A5_ITGA2_ITGB1 | COLLAGEN | CRC | AD |
COL4A5 | ITGA3_ITGB1 | COL4A5_ITGA3_ITGB1 | COLLAGEN | CRC | AD |
COL4A5 | ITGA11_ITGB1 | COL4A5_ITGA11_ITGB1 | COLLAGEN | CRC | AD |
COL4A5 | CD44 | COL4A5_CD44 | COLLAGEN | CRC | AD |
COL4A5 | SDC1 | COL4A5_SDC1 | COLLAGEN | CRC | AD |
COL4A5 | SDC4 | COL4A5_SDC4 | COLLAGEN | CRC | AD |
COL4A5 | ITGA1_ITGB1 | COL4A5_ITGA1_ITGB1 | COLLAGEN | CRC | ADJ |
COL4A5 | ITGA2_ITGB1 | COL4A5_ITGA2_ITGB1 | COLLAGEN | CRC | ADJ |
COL4A5 | ITGA3_ITGB1 | COL4A5_ITGA3_ITGB1 | COLLAGEN | CRC | ADJ |
COL4A5 | CD44 | COL4A5_CD44 | COLLAGEN | CRC | ADJ |
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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 |
COL4A5 | SNV | Missense_Mutation | c.3062N>A | p.Gly1021Glu | p.G1021E | P29400 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
COL4A5 | SNV | Missense_Mutation | c.3515N>T | p.Asp1172Val | p.D1172V | P29400 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-CM-5860-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | SD | |
COL4A5 | SNV | Missense_Mutation | rs752399898 | c.1435N>T | p.Asp479Tyr | p.D479Y | P29400 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-DM-A0X9-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
COL4A5 | SNV | Missense_Mutation | c.1107N>C | p.Glu369Asp | p.E369D | P29400 | protein_coding | tolerated(0.6) | benign(0.007) | TCGA-DM-A1D9-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
COL4A5 | SNV | Missense_Mutation | c.62N>A | p.Gly21Glu | p.G21E | P29400 | protein_coding | tolerated(1) | possibly_damaging(0.696) | TCGA-F4-6569-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |
COL4A5 | SNV | Missense_Mutation | c.2260G>C | p.Ala754Pro | p.A754P | P29400 | protein_coding | deleterious(0.02) | benign(0.113) | TCGA-QL-A97D-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
COL4A5 | SNV | Missense_Mutation | rs768320352 | c.4757C>T | p.Thr1586Met | p.T1586M | P29400 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
COL4A5 | SNV | Missense_Mutation | c.4566G>C | p.Met1522Ile | p.M1522I | P29400 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AG-3896-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
COL4A5 | SNV | Missense_Mutation | rs104886082 | c.920G>A | p.Gly307Asp | p.G307D | P29400 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
COL4A5 | SNV | Missense_Mutation | c.2176N>T | p.Ala726Ser | p.A726S | P29400 | protein_coding | tolerated(0.79) | benign(0.005) | TCGA-DY-A1H8-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | 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 |
1287 | COL4A5 | DRUGGABLE GENOME | CHEMBL2108709 | COLLAGENASE CLOSTRIDIUM HISTOLYTICUM | ||
1287 | COL4A5 | DRUGGABLE GENOME | CHEMBL2095222 | OCRIPLASMIN |
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