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Gene: COL15A1 |
Gene summary for COL15A1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | COL15A1 | Gene ID | 1306 |
Gene name | collagen type XV alpha 1 chain | |
Gene Alias | COL15A1 | |
Cytomap | 9q22.33 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | B3KTP7 |
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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 |
1306 | COL15A1 | PTC07 | Human | Thyroid | PTC | 3.89e-02 | 2.60e-02 | 0.2044 |
1306 | COL15A1 | ATC11 | Human | Thyroid | ATC | 1.88e-02 | 6.96e-01 | 0.3386 |
1306 | COL15A1 | ATC12 | Human | Thyroid | ATC | 8.04e-23 | 1.50e+00 | 0.34 |
1306 | COL15A1 | ATC3 | Human | Thyroid | ATC | 8.44e-03 | 6.06e-01 | 0.338 |
1306 | COL15A1 | ATC4 | Human | Thyroid | ATC | 7.89e-25 | 1.88e+00 | 0.34 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0002064112 | Thyroid | PTC | epithelial cell development | 101/5968 | 220/18723 | 8.53e-06 | 9.74e-05 | 101 |
GO:000188519 | Thyroid | PTC | endothelial cell development | 37/5968 | 64/18723 | 1.62e-05 | 1.70e-04 | 37 |
GO:00301986 | Thyroid | PTC | extracellular matrix organization | 124/5968 | 301/18723 | 3.75e-04 | 2.53e-03 | 124 |
GO:00430626 | Thyroid | PTC | extracellular structure organization | 124/5968 | 302/18723 | 4.38e-04 | 2.92e-03 | 124 |
GO:0003158111 | Thyroid | PTC | endothelium development | 62/5968 | 136/18723 | 5.45e-04 | 3.48e-03 | 62 |
GO:004544619 | Thyroid | PTC | endothelial cell differentiation | 55/5968 | 118/18723 | 5.64e-04 | 3.59e-03 | 55 |
GO:00452296 | Thyroid | PTC | external encapsulating structure organization | 124/5968 | 304/18723 | 5.96e-04 | 3.79e-03 | 124 |
GO:003019812 | Thyroid | ATC | extracellular matrix organization | 152/6293 | 301/18723 | 8.63e-10 | 2.24e-08 | 152 |
GO:004306212 | Thyroid | ATC | extracellular structure organization | 152/6293 | 302/18723 | 1.17e-09 | 2.94e-08 | 152 |
GO:004522912 | Thyroid | ATC | external encapsulating structure organization | 152/6293 | 304/18723 | 2.11e-09 | 5.08e-08 | 152 |
GO:000206428 | Thyroid | ATC | epithelial cell development | 103/6293 | 220/18723 | 3.06e-05 | 2.55e-04 | 103 |
GO:000188526 | Thyroid | ATC | endothelial cell development | 36/6293 | 64/18723 | 1.62e-04 | 1.11e-03 | 36 |
GO:000315825 | Thyroid | ATC | endothelium development | 66/6293 | 136/18723 | 2.16e-04 | 1.42e-03 | 66 |
GO:004544623 | Thyroid | ATC | endothelial cell differentiation | 56/6293 | 118/18723 | 1.23e-03 | 6.44e-03 | 56 |
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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 |
COL15A1 | SNV | Missense_Mutation | rs199564502 | c.308G>A | p.Arg103His | p.R103H | P39059 | protein_coding | tolerated(0.15) | benign(0.056) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
COL15A1 | SNV | Missense_Mutation | c.3265N>A | p.Phe1089Ile | p.F1089I | P39059 | protein_coding | tolerated(0.21) | benign(0.062) | TCGA-D7-6822-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
COL15A1 | SNV | Missense_Mutation | c.3710N>A | p.Cys1237Tyr | p.C1237Y | P39059 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-F1-6874-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
COL15A1 | SNV | Missense_Mutation | c.3371N>A | p.Gly1124Glu | p.G1124E | P39059 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-HU-A4GU-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
COL15A1 | SNV | Missense_Mutation | novel | c.656N>G | p.Leu219Arg | p.L219R | P39059 | protein_coding | deleterious(0) | benign(0.226) | TCGA-R5-A7O7-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
COL15A1 | SNV | Missense_Mutation | c.1577N>A | p.Ser526Tyr | p.S526Y | P39059 | protein_coding | tolerated_low_confidence(0.33) | benign(0.011) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | ||
COL15A1 | SNV | Missense_Mutation | novel | c.2275C>G | p.Pro759Ala | p.P759A | P39059 | protein_coding | tolerated(0.05) | probably_damaging(0.991) | TCGA-VQ-A8PH-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | PD |
COL15A1 | insertion | Frame_Shift_Ins | novel | c.291_292insA | p.Pro99AlafsTer14 | p.P99Afs*14 | P39059 | protein_coding | TCGA-BR-6802-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Ancillary | leucovorin | CR | ||
COL15A1 | deletion | Frame_Shift_Del | novel | c.3294delN | p.Pro1101ArgfsTer52 | p.P1101Rfs*52 | P39059 | protein_coding | TCGA-BR-8372-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | etoposide | CR | ||
COL15A1 | insertion | Nonsense_Mutation | novel | c.3214_3215insGTTGCACAGCTAGGCAGTAGTGCAACCAGGA | p.Val1072GlyfsTer7 | p.V1072Gfs*7 | P39059 | protein_coding | TCGA-CG-4444-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
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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 |
1306 | COL15A1 | DRUGGABLE GENOME | CHEMBL2108709 | COLLAGENASE CLOSTRIDIUM HISTOLYTICUM | ||
1306 | COL15A1 | DRUGGABLE GENOME | CHEMBL2095222 | OCRIPLASMIN |
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