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Gene: VPS13A |
Gene summary for VPS13A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VPS13A | Gene ID | 23230 |
| Gene name | vacuolar protein sorting 13 homolog A | |
| Gene Alias | CHAC | |
| Cytomap | 9q21.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q96RL7 |
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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 |
| 23230 | VPS13A | HTA11_3410_2000001011 | Human | Colorectum | AD | 9.82e-24 | -7.16e-01 | 0.0155 |
| 23230 | VPS13A | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.78e-02 | -4.96e-01 | -0.1207 |
| 23230 | VPS13A | HTA11_696_2000001011 | Human | Colorectum | AD | 5.62e-06 | -3.92e-01 | -0.1464 |
| 23230 | VPS13A | HTA11_866_2000001011 | Human | Colorectum | AD | 1.03e-04 | -3.90e-01 | -0.1001 |
| 23230 | VPS13A | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.10e-02 | -6.32e-01 | -0.2061 |
| 23230 | VPS13A | HTA11_7862_2000001011 | Human | Colorectum | AD | 7.36e-05 | -6.81e-01 | -0.0179 |
| 23230 | VPS13A | HTA11_866_3004761011 | Human | Colorectum | AD | 1.15e-12 | -6.03e-01 | 0.096 |
| 23230 | VPS13A | HTA11_9408_2000001011 | Human | Colorectum | AD | 8.13e-03 | -8.51e-01 | 0.0451 |
| 23230 | VPS13A | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.16e-10 | -6.40e-01 | 0.0338 |
| 23230 | VPS13A | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.47e-11 | -4.47e-01 | 0.0674 |
| 23230 | VPS13A | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.09e-15 | -4.88e-01 | 0.294 |
| 23230 | VPS13A | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 4.79e-03 | 7.89e-01 | 0.3487 |
| 23230 | VPS13A | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.13e-03 | 5.23e-01 | 0.281 |
| 23230 | VPS13A | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.86e-02 | -5.22e-01 | 0.2585 |
| 23230 | VPS13A | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.75e-25 | -6.37e-01 | 0.3005 |
| 23230 | VPS13A | A015-C-203 | Human | Colorectum | FAP | 3.23e-35 | -3.44e-01 | -0.1294 |
| 23230 | VPS13A | A015-C-204 | Human | Colorectum | FAP | 2.17e-05 | -5.45e-02 | -0.0228 |
| 23230 | VPS13A | A014-C-040 | Human | Colorectum | FAP | 1.70e-05 | -4.55e-01 | -0.1184 |
| 23230 | VPS13A | A002-C-201 | Human | Colorectum | FAP | 8.03e-13 | -2.05e-01 | 0.0324 |
| 23230 | VPS13A | A002-C-203 | Human | Colorectum | FAP | 2.63e-03 | -2.64e-02 | 0.2786 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 |
| 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: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:0016482 | Colorectum | AD | cytosolic transport | 68/3918 | 168/18723 | 6.00e-09 | 3.72e-07 | 68 |
| GO:0006605 | Colorectum | AD | protein targeting | 105/3918 | 314/18723 | 1.39e-07 | 6.44e-06 | 105 |
| GO:0006892 | Colorectum | AD | post-Golgi vesicle-mediated transport | 45/3918 | 104/18723 | 2.22e-07 | 9.26e-06 | 45 |
| GO:0007034 | Colorectum | AD | vacuolar transport | 60/3918 | 157/18723 | 4.97e-07 | 1.85e-05 | 60 |
| GO:0072665 | Colorectum | AD | protein localization to vacuole | 27/3918 | 67/18723 | 2.40e-04 | 3.04e-03 | 27 |
| GO:0032507 | Colorectum | AD | maintenance of protein location in cell | 25/3918 | 65/18723 | 9.12e-04 | 8.71e-03 | 25 |
| GO:0034067 | Colorectum | AD | protein localization to Golgi apparatus | 14/3918 | 29/18723 | 9.40e-04 | 8.92e-03 | 14 |
| GO:0051651 | Colorectum | AD | maintenance of location in cell | 61/3918 | 214/18723 | 5.02e-03 | 3.37e-02 | 61 |
| GO:0006623 | Colorectum | AD | protein targeting to vacuole | 15/3918 | 37/18723 | 5.24e-03 | 3.47e-02 | 15 |
| GO:0072666 | Colorectum | AD | establishment of protein localization to vacuole | 18/3918 | 49/18723 | 7.93e-03 | 4.73e-02 | 18 |
| GO:0045185 | Colorectum | AD | maintenance of protein location | 30/3918 | 94/18723 | 8.26e-03 | 4.85e-02 | 30 |
| GO:00725942 | Colorectum | MSS | establishment of protein localization to organelle | 139/3467 | 422/18723 | 5.75e-13 | 1.12e-10 | 139 |
| GO:00481932 | Colorectum | MSS | Golgi vesicle transport | 101/3467 | 296/18723 | 9.09e-11 | 9.77e-09 | 101 |
| GO:00066052 | Colorectum | MSS | protein targeting | 97/3467 | 314/18723 | 6.76e-08 | 3.46e-06 | 97 |
| GO:00164822 | Colorectum | MSS | cytosolic transport | 59/3467 | 168/18723 | 2.29e-07 | 9.79e-06 | 59 |
| GO:00068922 | Colorectum | MSS | post-Golgi vesicle-mediated transport | 40/3467 | 104/18723 | 1.45e-06 | 4.82e-05 | 40 |
| GO:00070342 | Colorectum | MSS | vacuolar transport | 52/3467 | 157/18723 | 8.25e-06 | 2.07e-04 | 52 |
| GO:00726652 | Colorectum | MSS | protein localization to vacuole | 23/3467 | 67/18723 | 1.51e-03 | 1.39e-02 | 23 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 |
| VPS13A | SNV | Missense_Mutation | c.6793N>A | p.Asp2265Asn | p.D2265N | Q96RL7 | protein_coding | tolerated(0.07) | probably_damaging(0.975) | TCGA-A2-A0CL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| VPS13A | SNV | Missense_Mutation | c.2969N>T | p.Asn990Ile | p.N990I | Q96RL7 | protein_coding | tolerated(0.07) | possibly_damaging(0.866) | TCGA-A2-A0EV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| VPS13A | SNV | Missense_Mutation | c.1254N>C | p.Lys418Asn | p.K418N | Q96RL7 | protein_coding | deleterious(0.01) | benign(0.149) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VPS13A | SNV | Missense_Mutation | c.1482N>C | p.Leu494Phe | p.L494F | Q96RL7 | protein_coding | deleterious(0) | probably_damaging(0.951) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VPS13A | SNV | Missense_Mutation | c.1646N>T | p.Ser549Leu | p.S549L | Q96RL7 | protein_coding | tolerated(0.36) | benign(0) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VPS13A | SNV | Missense_Mutation | novel | c.9183N>T | p.Met3061Ile | p.M3061I | Q96RL7 | protein_coding | tolerated(0.17) | benign(0.013) | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| VPS13A | SNV | Missense_Mutation | novel | c.6256N>T | p.Asp2086Tyr | p.D2086Y | Q96RL7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VPS13A | SNV | Missense_Mutation | rs777520036 | c.9377N>A | p.Arg3126Lys | p.R3126K | Q96RL7 | protein_coding | tolerated(0.17) | benign(0.078) | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| VPS13A | SNV | Missense_Mutation | c.6948N>C | p.Met2316Ile | p.M2316I | Q96RL7 | protein_coding | tolerated(0.26) | benign(0.009) | TCGA-BH-A0AV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
| VPS13A | SNV | Missense_Mutation | c.6988N>A | p.Glu2330Lys | p.E2330K | Q96RL7 | protein_coding | tolerated(0.52) | benign(0.328) | TCGA-BH-A0B4-01 | Breast | breast invasive carcinoma | Male | >=65 | III/IV | Hormone Therapy | tamoxiphen | 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 32 33 34 35 36 37 |
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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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