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Gene: VPS13A |
Gene summary for VPS13A |
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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 |
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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 |
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∗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 |
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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 |
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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 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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.3521A>C | p.Asn1174Thr | p.N1174T | Q96RL7 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
VPS13A | SNV | Missense_Mutation | c.4280T>G | p.Leu1427Arg | p.L1427R | Q96RL7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
VPS13A | SNV | Missense_Mutation | rs769826126 | c.1447N>C | p.Lys483Gln | p.K483Q | Q96RL7 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-A01Z-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
VPS13A | SNV | Missense_Mutation | c.8438N>T | p.Ala2813Val | p.A2813V | Q96RL7 | protein_coding | tolerated(0.1) | possibly_damaging(0.87) | TCGA-AD-6901-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |
VPS13A | SNV | Missense_Mutation | c.4659N>T | p.Glu1553Asp | p.E1553D | Q96RL7 | protein_coding | deleterious(0.04) | possibly_damaging(0.855) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VPS13A | SNV | Missense_Mutation | novel | c.707N>C | p.Lys236Thr | p.K236T | Q96RL7 | protein_coding | deleterious(0) | benign(0.246) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
VPS13A | SNV | Missense_Mutation | rs746836759 | c.2192G>A | p.Arg731Gln | p.R731Q | Q96RL7 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VPS13A | SNV | Missense_Mutation | novel | c.135A>C | p.Glu45Asp | p.E45D | Q96RL7 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
VPS13A | SNV | Missense_Mutation | novel | c.3295A>C | p.Asn1099His | p.N1099H | Q96RL7 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
VPS13A | SNV | Missense_Mutation | c.6195G>T | p.Lys2065Asn | p.K2065N | Q96RL7 | protein_coding | tolerated(0.09) | benign(0.209) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | 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 |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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