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Gene: VPS13C |
Gene summary for VPS13C |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VPS13C | Gene ID | 54832 |
| Gene name | vacuolar protein sorting 13 homolog C | |
| Gene Alias | PARK23 | |
| Cytomap | 15q22.2 | |
| Gene Type | protein-coding | GO ID | GO:0000422 | UniProtAcc | Q709C8 |
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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 |
| 54832 | VPS13C | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.38e-19 | -5.97e-01 | 0.0155 |
| 54832 | VPS13C | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.34e-05 | -4.92e-01 | -0.1808 |
| 54832 | VPS13C | HTA11_2951_2000001011 | Human | Colorectum | AD | 5.38e-03 | -6.95e-01 | 0.0216 |
| 54832 | VPS13C | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.01e-09 | -6.50e-01 | -0.1207 |
| 54832 | VPS13C | HTA11_83_2000001011 | Human | Colorectum | SER | 3.20e-03 | -4.07e-01 | -0.1526 |
| 54832 | VPS13C | HTA11_696_2000001011 | Human | Colorectum | AD | 3.05e-10 | -4.73e-01 | -0.1464 |
| 54832 | VPS13C | HTA11_866_2000001011 | Human | Colorectum | AD | 7.23e-07 | -4.28e-01 | -0.1001 |
| 54832 | VPS13C | HTA11_5212_2000001011 | Human | Colorectum | AD | 3.82e-04 | -6.80e-01 | -0.2061 |
| 54832 | VPS13C | HTA11_5216_2000001011 | Human | Colorectum | SER | 7.67e-04 | -7.86e-01 | -0.1462 |
| 54832 | VPS13C | HTA11_546_2000001011 | Human | Colorectum | AD | 2.91e-02 | -4.50e-01 | -0.0842 |
| 54832 | VPS13C | HTA11_866_3004761011 | Human | Colorectum | AD | 7.63e-04 | -3.24e-01 | 0.096 |
| 54832 | VPS13C | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.05e-12 | -6.06e-01 | 0.0338 |
| 54832 | VPS13C | HTA11_7696_3000711011 | Human | Colorectum | AD | 5.19e-06 | -4.05e-01 | 0.0674 |
| 54832 | VPS13C | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.17e-10 | -4.49e-01 | 0.3859 |
| 54832 | VPS13C | HTA11_99999973899_84307 | Human | Colorectum | MSS | 3.81e-04 | -4.70e-01 | 0.2585 |
| 54832 | VPS13C | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.47e-08 | -3.87e-01 | 0.3005 |
| 54832 | VPS13C | F007 | Human | Colorectum | FAP | 2.87e-03 | 1.69e-01 | 0.1176 |
| 54832 | VPS13C | A001-C-207 | Human | Colorectum | FAP | 2.50e-03 | 2.14e-01 | 0.1278 |
| 54832 | VPS13C | A015-C-203 | Human | Colorectum | FAP | 9.24e-30 | -2.13e-01 | -0.1294 |
| 54832 | VPS13C | A015-C-204 | Human | Colorectum | FAP | 3.22e-04 | -1.53e-01 | -0.0228 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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 |
| 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:0072594 | Colorectum | AD | establishment of protein localization to organelle | 148/3918 | 422/18723 | 7.95e-12 | 1.04e-09 | 148 |
| GO:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
| GO:0022411 | Colorectum | AD | cellular component disassembly | 147/3918 | 443/18723 | 8.53e-10 | 6.76e-08 | 147 |
| GO:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
| GO:0016482 | Colorectum | AD | cytosolic transport | 68/3918 | 168/18723 | 6.00e-09 | 3.72e-07 | 68 |
| GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
| GO:0006605 | Colorectum | AD | protein targeting | 105/3918 | 314/18723 | 1.39e-07 | 6.44e-06 | 105 |
| GO:0032868 | Colorectum | AD | response to insulin | 91/3918 | 264/18723 | 2.02e-07 | 8.48e-06 | 91 |
| GO:0006892 | Colorectum | AD | post-Golgi vesicle-mediated transport | 45/3918 | 104/18723 | 2.22e-07 | 9.26e-06 | 45 |
| GO:0010821 | Colorectum | AD | regulation of mitochondrion organization | 57/3918 | 144/18723 | 2.43e-07 | 9.92e-06 | 57 |
| GO:0007034 | Colorectum | AD | vacuolar transport | 60/3918 | 157/18723 | 4.97e-07 | 1.85e-05 | 60 |
| GO:1903008 | Colorectum | AD | organelle disassembly | 46/3918 | 114/18723 | 1.81e-06 | 5.48e-05 | 46 |
| GO:0043434 | Colorectum | AD | response to peptide hormone | 126/3918 | 414/18723 | 2.70e-06 | 7.86e-05 | 126 |
| GO:1903146 | Colorectum | AD | regulation of autophagy of mitochondrion | 19/3918 | 33/18723 | 4.52e-06 | 1.21e-04 | 19 |
| GO:0000422 | Colorectum | AD | autophagy of mitochondrion | 35/3918 | 81/18723 | 4.94e-06 | 1.29e-04 | 35 |
| GO:0061726 | Colorectum | AD | mitochondrion disassembly | 35/3918 | 81/18723 | 4.94e-06 | 1.29e-04 | 35 |
| GO:0061912 | Colorectum | AD | selective autophagy | 29/3918 | 68/18723 | 4.20e-05 | 7.39e-04 | 29 |
| GO:0016241 | Colorectum | AD | regulation of macroautophagy | 50/3918 | 141/18723 | 4.55e-05 | 7.92e-04 | 50 |
| GO:0072665 | Colorectum | AD | protein localization to vacuole | 27/3918 | 67/18723 | 2.40e-04 | 3.04e-03 | 27 |
| GO:0000423 | Colorectum | AD | mitophagy | 14/3918 | 28/18723 | 6.01e-04 | 6.33e-03 | 14 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 |
| 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 |
| 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 |
| VPS13C | SNV | Missense_Mutation | novel | c.4199C>T | p.Ser1400Leu | p.S1400L | Q709C8 | protein_coding | tolerated(0.26) | benign(0) | TCGA-AC-A6IX-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| VPS13C | SNV | Missense_Mutation | c.9901N>G | p.Gln3301Glu | p.Q3301E | Q709C8 | protein_coding | tolerated(0.76) | benign(0) | TCGA-AR-A0TU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Doxorubicin | SD | |
| VPS13C | SNV | Missense_Mutation | c.6452N>G | p.Val2151Gly | p.V2151G | Q709C8 | protein_coding | deleterious(0) | possibly_damaging(0.677) | TCGA-AR-A251-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| VPS13C | SNV | Missense_Mutation | novel | c.725C>T | p.Ala242Val | p.A242V | Q709C8 | protein_coding | deleterious(0.02) | benign(0.053) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| VPS13C | SNV | Missense_Mutation | rs753815184 | c.11195N>T | p.Thr3732Met | p.T3732M | Q709C8 | protein_coding | tolerated(0.3) | benign(0.003) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VPS13C | SNV | Missense_Mutation | novel | c.3176N>T | p.Ser1059Leu | p.S1059L | Q709C8 | protein_coding | tolerated(0.33) | benign(0.001) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| VPS13C | SNV | Missense_Mutation | rs758856957 | c.1099N>G | p.His367Asp | p.H367D | Q709C8 | protein_coding | deleterious(0) | benign(0.421) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| VPS13C | SNV | Missense_Mutation | c.4840G>T | p.Asp1614Tyr | p.D1614Y | Q709C8 | protein_coding | deleterious(0) | probably_damaging(0.94) | TCGA-C8-A12Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| VPS13C | SNV | Missense_Mutation | rs753815184 | c.11195N>T | p.Thr3732Met | p.T3732M | Q709C8 | protein_coding | tolerated(0.3) | benign(0.003) | TCGA-C8-A1HG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| VPS13C | SNV | Missense_Mutation | rs562241298 | c.10011G>C | p.Leu3337Phe | p.L3337F | Q709C8 | protein_coding | deleterious(0.01) | probably_damaging(0.917) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR |
| 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 32 33 34 35 36 37 38 39 40 41 |
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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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