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Gene: VPS39 |
Gene summary for VPS39 |
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Gene information | Species | Human | Gene symbol | VPS39 | Gene ID | 23339 |
Gene name | VPS39 subunit of HOPS complex | |
Gene Alias | TLP | |
Cytomap | 15q15.1 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q96JC1 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
23339 | VPS39 | LZE2T | Human | Esophagus | ESCC | 5.49e-03 | 4.14e-01 | 0.082 |
23339 | VPS39 | LZE4T | Human | Esophagus | ESCC | 8.16e-06 | 1.90e-01 | 0.0811 |
23339 | VPS39 | LZE7T | Human | Esophagus | ESCC | 2.88e-02 | 1.62e-01 | 0.0667 |
23339 | VPS39 | LZE20T | Human | Esophagus | ESCC | 7.21e-03 | 9.02e-02 | 0.0662 |
23339 | VPS39 | LZE24T | Human | Esophagus | ESCC | 8.81e-12 | 2.72e-01 | 0.0596 |
23339 | VPS39 | LZE21T | Human | Esophagus | ESCC | 2.52e-02 | 2.02e-01 | 0.0655 |
23339 | VPS39 | P1T-E | Human | Esophagus | ESCC | 8.15e-06 | 3.47e-01 | 0.0875 |
23339 | VPS39 | P2T-E | Human | Esophagus | ESCC | 2.20e-12 | 1.74e-01 | 0.1177 |
23339 | VPS39 | P4T-E | Human | Esophagus | ESCC | 7.25e-14 | 2.76e-01 | 0.1323 |
23339 | VPS39 | P5T-E | Human | Esophagus | ESCC | 4.76e-05 | 8.80e-02 | 0.1327 |
23339 | VPS39 | P8T-E | Human | Esophagus | ESCC | 8.80e-19 | 2.92e-01 | 0.0889 |
23339 | VPS39 | P9T-E | Human | Esophagus | ESCC | 3.27e-14 | 2.07e-01 | 0.1131 |
23339 | VPS39 | P10T-E | Human | Esophagus | ESCC | 2.75e-16 | 3.13e-01 | 0.116 |
23339 | VPS39 | P11T-E | Human | Esophagus | ESCC | 9.33e-04 | 2.14e-01 | 0.1426 |
23339 | VPS39 | P12T-E | Human | Esophagus | ESCC | 5.82e-20 | 2.68e-01 | 0.1122 |
23339 | VPS39 | P15T-E | Human | Esophagus | ESCC | 1.49e-17 | 2.32e-01 | 0.1149 |
23339 | VPS39 | P16T-E | Human | Esophagus | ESCC | 6.42e-16 | 2.30e-01 | 0.1153 |
23339 | VPS39 | P19T-E | Human | Esophagus | ESCC | 3.34e-08 | 4.11e-01 | 0.1662 |
23339 | VPS39 | P20T-E | Human | Esophagus | ESCC | 4.90e-13 | 1.86e-01 | 0.1124 |
23339 | VPS39 | P21T-E | Human | Esophagus | ESCC | 9.67e-18 | 2.67e-01 | 0.1617 |
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Tissue | Expression Dynamics | Abbreviation |
Esophagus | ![]() | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias | ||
LGIN: Low-grade intraepithelial neoplasias |
∗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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
GO:001619715 | Esophagus | ESCC | endosomal transport | 168/8552 | 230/18723 | 2.28e-17 | 1.93e-15 | 168 |
GO:000703417 | Esophagus | ESCC | vacuolar transport | 119/8552 | 157/18723 | 1.16e-14 | 6.30e-13 | 119 |
GO:009887615 | Esophagus | ESCC | vesicle-mediated transport to the plasma membrane | 99/8552 | 136/18723 | 1.13e-10 | 3.39e-09 | 99 |
GO:00070419 | Esophagus | ESCC | lysosomal transport | 83/8552 | 114/18723 | 3.52e-09 | 7.41e-08 | 83 |
GO:00482844 | Esophagus | ESCC | organelle fusion | 94/8552 | 141/18723 | 3.72e-07 | 5.16e-06 | 94 |
GO:00901743 | Esophagus | ESCC | organelle membrane fusion | 73/8552 | 110/18723 | 9.29e-06 | 8.88e-05 | 73 |
GO:00069063 | Esophagus | ESCC | vesicle fusion | 70/8552 | 106/18723 | 1.82e-05 | 1.60e-04 | 70 |
GO:00324565 | Esophagus | ESCC | endocytic recycling | 51/8552 | 73/18723 | 2.47e-05 | 2.10e-04 | 51 |
GO:00083333 | Esophagus | ESCC | endosome to lysosome transport | 40/8552 | 55/18723 | 4.27e-05 | 3.42e-04 | 40 |
GO:00610254 | Esophagus | ESCC | membrane fusion | 98/8552 | 163/18723 | 1.39e-04 | 9.41e-04 | 98 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05132211 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
hsa05132310 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
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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 |
VPS39 | SNV | Missense_Mutation | rs191703716 | c.1753N>T | p.Arg585Cys | p.R585C | Q96JC1 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-86-8281-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
VPS39 | SNV | Missense_Mutation | c.1256N>G | p.Tyr419Cys | p.Y419C | Q96JC1 | protein_coding | deleterious(0) | possibly_damaging(0.898) | TCGA-NJ-A4YI-01 | Lung | lung adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
VPS39 | SNV | Missense_Mutation | novel | c.361N>T | p.Thr121Ser | p.T121S | Q96JC1 | protein_coding | tolerated(0.45) | benign(0.04) | TCGA-21-1079-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
VPS39 | SNV | Missense_Mutation | c.2566N>G | p.Lys856Glu | p.K856E | Q96JC1 | protein_coding | deleterious(0.03) | benign(0.048) | TCGA-39-5028-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
VPS39 | SNV | Missense_Mutation | c.1437G>T | p.Leu479Phe | p.L479F | Q96JC1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-46-3768-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Chemotherapy | carboplatin | SD | |
VPS39 | SNV | Missense_Mutation | novel | c.1612N>T | p.Arg538Trp | p.R538W | Q96JC1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-56-8628-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
VPS39 | SNV | Missense_Mutation | novel | c.395N>C | p.Glu132Ala | p.E132A | Q96JC1 | protein_coding | tolerated(0.76) | benign(0) | TCGA-60-2715-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | docetaxel | PD |
VPS39 | SNV | Missense_Mutation | c.331N>A | p.Val111Ile | p.V111I | Q96JC1 | protein_coding | tolerated(0.24) | benign(0) | TCGA-66-2758-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | cisplatin | CR | |
VPS39 | SNV | Missense_Mutation | novel | c.1604N>A | p.Gly535Asp | p.G535D | Q96JC1 | protein_coding | deleterious(0.02) | probably_damaging(0.924) | TCGA-90-A4ED-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
VPS39 | SNV | Missense_Mutation | novel | c.2405N>C | p.Ile802Thr | p.I802T | Q96JC1 | protein_coding | tolerated(0.68) | benign(0.001) | TCGA-94-8491-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | unknown | PD |
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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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