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Gene: VPS33A |
Gene summary for VPS33A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VPS33A | Gene ID | 65082 |
| Gene name | VPS33A core subunit of CORVET and HOPS complexes | |
| Gene Alias | MPSPS | |
| Cytomap | 12q24.31 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q96AX1 |
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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 |
| 65082 | VPS33A | C04 | Human | Oral cavity | OSCC | 1.95e-06 | 3.52e-01 | 0.2633 |
| 65082 | VPS33A | C21 | Human | Oral cavity | OSCC | 3.08e-16 | 3.66e-01 | 0.2678 |
| 65082 | VPS33A | C30 | Human | Oral cavity | OSCC | 9.54e-12 | 5.27e-01 | 0.3055 |
| 65082 | VPS33A | C38 | Human | Oral cavity | OSCC | 2.48e-02 | 3.96e-01 | 0.172 |
| 65082 | VPS33A | C43 | Human | Oral cavity | OSCC | 1.75e-03 | 1.44e-01 | 0.1704 |
| 65082 | VPS33A | C46 | Human | Oral cavity | OSCC | 7.93e-08 | 2.45e-01 | 0.1673 |
| 65082 | VPS33A | C08 | Human | Oral cavity | OSCC | 3.22e-08 | 2.32e-01 | 0.1919 |
| 65082 | VPS33A | LN22 | Human | Oral cavity | OSCC | 2.53e-02 | 3.38e-01 | 0.1733 |
| 65082 | VPS33A | LN46 | Human | Oral cavity | OSCC | 4.56e-03 | 1.78e-01 | 0.1666 |
| 65082 | VPS33A | LP15 | Human | Oral cavity | LP | 1.60e-03 | 5.77e-01 | 0.2174 |
| 65082 | VPS33A | SYSMH2 | Human | Oral cavity | OSCC | 2.18e-04 | 1.76e-01 | 0.2326 |
| 65082 | VPS33A | SYSMH3 | Human | Oral cavity | OSCC | 3.30e-09 | 2.21e-01 | 0.2442 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:002241119 | Oral cavity | OSCC | cellular component disassembly | 283/7305 | 443/18723 | 9.57e-27 | 3.37e-24 | 283 |
| GO:001623610 | Oral cavity | OSCC | macroautophagy | 192/7305 | 291/18723 | 7.01e-21 | 1.14e-18 | 192 |
| GO:00070335 | Oral cavity | OSCC | vacuole organization | 115/7305 | 180/18723 | 1.11e-11 | 4.00e-10 | 115 |
| GO:003009920 | Oral cavity | OSCC | myeloid cell differentiation | 213/7305 | 381/18723 | 1.24e-11 | 4.42e-10 | 213 |
| GO:000703410 | Oral cavity | OSCC | vacuolar transport | 103/7305 | 157/18723 | 1.25e-11 | 4.44e-10 | 103 |
| GO:003298410 | Oral cavity | OSCC | protein-containing complex disassembly | 136/7305 | 224/18723 | 3.42e-11 | 1.13e-09 | 136 |
| GO:00516489 | Oral cavity | OSCC | vesicle localization | 105/7305 | 177/18723 | 3.30e-08 | 6.30e-07 | 105 |
| GO:00070402 | Oral cavity | OSCC | lysosome organization | 51/7305 | 74/18723 | 1.77e-07 | 2.87e-06 | 51 |
| GO:00801712 | Oral cavity | OSCC | lytic vacuole organization | 51/7305 | 74/18723 | 1.77e-07 | 2.87e-06 | 51 |
| GO:00070418 | Oral cavity | OSCC | lysosomal transport | 69/7305 | 114/18723 | 2.62e-06 | 3.26e-05 | 69 |
| GO:00973522 | Oral cavity | OSCC | autophagosome maturation | 28/7305 | 40/18723 | 7.00e-05 | 5.60e-04 | 28 |
| GO:00357512 | Oral cavity | OSCC | regulation of lysosomal lumen pH | 14/7305 | 16/18723 | 9.15e-05 | 6.93e-04 | 14 |
| GO:0033059 | Oral cavity | OSCC | cellular pigmentation | 33/7305 | 53/18723 | 5.11e-04 | 2.98e-03 | 33 |
| GO:00083332 | Oral cavity | OSCC | endosome to lysosome transport | 33/7305 | 55/18723 | 1.30e-03 | 6.46e-03 | 33 |
| GO:001623615 | Oral cavity | LP | macroautophagy | 135/4623 | 291/18723 | 4.71e-16 | 6.70e-14 | 135 |
| GO:0022411110 | Oral cavity | LP | cellular component disassembly | 173/4623 | 443/18723 | 9.97e-12 | 7.44e-10 | 173 |
| GO:000703415 | Oral cavity | LP | vacuolar transport | 74/4623 | 157/18723 | 7.85e-10 | 3.70e-08 | 74 |
| GO:000703313 | Oral cavity | LP | vacuole organization | 79/4623 | 180/18723 | 1.26e-08 | 4.74e-07 | 79 |
| GO:000704114 | Oral cavity | LP | lysosomal transport | 49/4623 | 114/18723 | 1.38e-05 | 2.45e-04 | 49 |
| GO:0030099110 | Oral cavity | LP | myeloid cell differentiation | 130/4623 | 381/18723 | 1.94e-05 | 3.27e-04 | 130 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0513230 | Oral cavity | OSCC | Salmonella infection | 174/3704 | 249/8465 | 2.67e-17 | 1.49e-15 | 7.58e-16 | 174 |
| hsa05132114 | Oral cavity | OSCC | Salmonella infection | 174/3704 | 249/8465 | 2.67e-17 | 1.49e-15 | 7.58e-16 | 174 |
| hsa05132210 | Oral cavity | LP | Salmonella infection | 128/2418 | 249/8465 | 1.17e-14 | 2.79e-13 | 1.80e-13 | 128 |
| hsa0513238 | Oral cavity | LP | Salmonella infection | 128/2418 | 249/8465 | 1.17e-14 | 2.79e-13 | 1.80e-13 | 128 |
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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 |
| VPS33A | SNV | Missense_Mutation | novel | c.517T>C | p.Tyr173His | p.Y173H | Q96AX1 | protein_coding | tolerated(0.21) | benign(0.176) | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| VPS33A | SNV | Missense_Mutation | rs766589793 | c.430N>T | p.Leu144Phe | p.L144F | Q96AX1 | protein_coding | tolerated(0.32) | benign(0.02) | TCGA-QK-A6IG-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | III/IV | Chemotherapy | carboplatin | PD |
| VPS33A | SNV | Missense_Mutation | novel | c.419N>G | p.Tyr140Cys | p.Y140C | Q96AX1 | protein_coding | deleterious(0.04) | possibly_damaging(0.866) | TCGA-B7-A5TI-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | eloxatin | CR |
| VPS33A | SNV | Missense_Mutation | rs765189927 | c.8C>T | p.Ala3Val | p.A3V | Q96AX1 | protein_coding | tolerated(0.06) | benign(0.036) | TCGA-BR-4280-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| VPS33A | SNV | Missense_Mutation | c.20N>G | p.Tyr7Cys | p.Y7C | Q96AX1 | protein_coding | tolerated(0.08) | benign(0) | TCGA-BR-8363-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| VPS33A | SNV | Missense_Mutation | c.556T>C | p.Tyr186His | p.Y186H | Q96AX1 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BR-8372-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | etoposide | CR | |
| VPS33A | SNV | Missense_Mutation | rs150472752 | c.208C>T | p.Arg70Cys | p.R70C | Q96AX1 | protein_coding | tolerated(0.17) | benign(0.027) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | 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 |
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