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Gene: COL16A1 |
Gene summary for COL16A1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COL16A1 | Gene ID | 1307 |
| Gene name | collagen type XVI alpha 1 chain | |
| Gene Alias | 447AA | |
| Cytomap | 1p35.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q07092 |
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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 |
| 1307 | COL16A1 | LZE24T | Human | Esophagus | ESCC | 8.53e-13 | 2.25e-01 | 0.0596 |
| 1307 | COL16A1 | P2T-E | Human | Esophagus | ESCC | 2.14e-25 | 4.78e-01 | 0.1177 |
| 1307 | COL16A1 | P4T-E | Human | Esophagus | ESCC | 6.23e-07 | 1.63e-01 | 0.1323 |
| 1307 | COL16A1 | P5T-E | Human | Esophagus | ESCC | 2.59e-04 | 1.18e-01 | 0.1327 |
| 1307 | COL16A1 | P8T-E | Human | Esophagus | ESCC | 1.15e-09 | 1.84e-01 | 0.0889 |
| 1307 | COL16A1 | P10T-E | Human | Esophagus | ESCC | 5.86e-33 | 6.80e-01 | 0.116 |
| 1307 | COL16A1 | P11T-E | Human | Esophagus | ESCC | 2.94e-08 | 5.57e-01 | 0.1426 |
| 1307 | COL16A1 | P12T-E | Human | Esophagus | ESCC | 5.19e-12 | 1.97e-01 | 0.1122 |
| 1307 | COL16A1 | P15T-E | Human | Esophagus | ESCC | 2.07e-03 | 1.69e-01 | 0.1149 |
| 1307 | COL16A1 | P16T-E | Human | Esophagus | ESCC | 6.64e-07 | 7.32e-02 | 0.1153 |
| 1307 | COL16A1 | P19T-E | Human | Esophagus | ESCC | 3.89e-04 | 2.41e-01 | 0.1662 |
| 1307 | COL16A1 | P20T-E | Human | Esophagus | ESCC | 3.09e-13 | 3.18e-01 | 0.1124 |
| 1307 | COL16A1 | P21T-E | Human | Esophagus | ESCC | 8.47e-19 | 3.47e-01 | 0.1617 |
| 1307 | COL16A1 | P22T-E | Human | Esophagus | ESCC | 2.18e-08 | 1.53e-01 | 0.1236 |
| 1307 | COL16A1 | P23T-E | Human | Esophagus | ESCC | 2.00e-03 | 1.97e-01 | 0.108 |
| 1307 | COL16A1 | P24T-E | Human | Esophagus | ESCC | 9.52e-03 | 9.32e-02 | 0.1287 |
| 1307 | COL16A1 | P26T-E | Human | Esophagus | ESCC | 6.59e-08 | 1.57e-01 | 0.1276 |
| 1307 | COL16A1 | P27T-E | Human | Esophagus | ESCC | 1.03e-10 | 1.90e-01 | 0.1055 |
| 1307 | COL16A1 | P28T-E | Human | Esophagus | ESCC | 5.29e-08 | 1.47e-01 | 0.1149 |
| 1307 | COL16A1 | P31T-E | Human | Esophagus | ESCC | 5.64e-14 | 2.14e-01 | 0.1251 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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 | ||
| 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:0150115110 | Esophagus | ESCC | cell-substrate junction organization | 77/8552 | 101/18723 | 3.46e-10 | 9.57e-09 | 77 |
| GO:000704418 | Esophagus | ESCC | cell-substrate junction assembly | 73/8552 | 95/18723 | 5.27e-10 | 1.35e-08 | 73 |
| GO:003158919 | Esophagus | ESCC | cell-substrate adhesion | 221/8552 | 363/18723 | 3.06e-09 | 6.62e-08 | 221 |
| GO:001081020 | Esophagus | ESCC | regulation of cell-substrate adhesion | 144/8552 | 221/18723 | 3.55e-09 | 7.45e-08 | 144 |
| GO:004804116 | Esophagus | ESCC | focal adhesion assembly | 65/8552 | 87/18723 | 3.28e-08 | 6.08e-07 | 65 |
| GO:004578527 | Esophagus | ESCC | positive regulation of cell adhesion | 255/8552 | 437/18723 | 5.07e-08 | 9.11e-07 | 255 |
| GO:001081126 | Esophagus | ESCC | positive regulation of cell-substrate adhesion | 84/8552 | 123/18723 | 3.18e-07 | 4.50e-06 | 84 |
| GO:000195217 | Esophagus | ESCC | regulation of cell-matrix adhesion | 85/8552 | 128/18723 | 1.70e-06 | 2.02e-05 | 85 |
| GO:000716018 | Esophagus | ESCC | cell-matrix adhesion | 141/8552 | 233/18723 | 3.33e-06 | 3.71e-05 | 141 |
| GO:015011619 | Esophagus | ESCC | regulation of cell-substrate junction organization | 51/8552 | 71/18723 | 6.99e-06 | 7.04e-05 | 51 |
| GO:005189318 | Esophagus | ESCC | regulation of focal adhesion assembly | 47/8552 | 66/18723 | 2.31e-05 | 1.98e-04 | 47 |
| GO:009010918 | Esophagus | ESCC | regulation of cell-substrate junction assembly | 47/8552 | 66/18723 | 2.31e-05 | 1.98e-04 | 47 |
| GO:00301984 | Esophagus | ESCC | extracellular matrix organization | 171/8552 | 301/18723 | 6.08e-05 | 4.67e-04 | 171 |
| GO:00432007 | Esophagus | ESCC | response to amino acid | 74/8552 | 116/18723 | 6.23e-05 | 4.76e-04 | 74 |
| GO:000110110 | Esophagus | ESCC | response to acid chemical | 84/8552 | 135/18723 | 7.70e-05 | 5.74e-04 | 84 |
| 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:00712305 | Esophagus | ESCC | cellular response to amino acid stimulus | 48/8552 | 71/18723 | 1.55e-04 | 1.03e-03 | 48 |
| GO:000195418 | Esophagus | ESCC | positive regulation of cell-matrix adhesion | 40/8552 | 58/18723 | 2.83e-04 | 1.71e-03 | 40 |
| GO:00072299 | Esophagus | ESCC | integrin-mediated signaling pathway | 67/8552 | 107/18723 | 3.03e-04 | 1.81e-03 | 67 |
| Page: 1 2 3 4 5 6 7 |
| 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 |
| COL16A1 | SNV | Missense_Mutation | c.2224G>T | p.Gly742Trp | p.G742W | Q07092 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-A8-A097-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| COL16A1 | SNV | Missense_Mutation | novel | c.2005N>G | p.Pro669Ala | p.P669A | Q07092 | protein_coding | deleterious(0.01) | possibly_damaging(0.525) | TCGA-AR-A5QQ-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD |
| COL16A1 | SNV | Missense_Mutation | rs573984488 | c.233N>A | p.Arg78His | p.R78H | Q07092 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-B6-A400-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| COL16A1 | SNV | Missense_Mutation | c.2512N>T | p.Pro838Ser | p.P838S | Q07092 | protein_coding | tolerated(0.1) | benign(0.018) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| COL16A1 | SNV | Missense_Mutation | c.3994N>A | p.Gly1332Ser | p.G1332S | Q07092 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A0HN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| COL16A1 | SNV | Missense_Mutation | c.4054G>A | p.Glu1352Lys | p.E1352K | Q07092 | protein_coding | tolerated(0.11) | possibly_damaging(0.824) | TCGA-D8-A13Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| COL16A1 | SNV | Missense_Mutation | c.3941G>C | p.Gly1314Ala | p.G1314A | Q07092 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-E2-A10C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| COL16A1 | SNV | Missense_Mutation | c.4303N>G | p.Asn1435Asp | p.N1435D | Q07092 | protein_coding | tolerated(0.12) | possibly_damaging(0.874) | TCGA-EW-A1OZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | SD | |
| COL16A1 | insertion | Frame_Shift_Ins | novel | c.3043_3044insCAAGGCTGAAAGAAATGATTCTAAAATCA | p.Gly1015AlafsTer36 | p.G1015Afs*36 | Q07092 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| COL16A1 | insertion | In_Frame_Ins | novel | c.468_469insCCTTGGGCT | p.Cys156_Ile157insProTrpAla | p.C156_I157insPWA | Q07092 | protein_coding | TCGA-AN-A0FS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
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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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