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Gene: VPS39 |
Gene summary for VPS39 |
 Gene summary. |
| 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 |
| 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 |
| 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 |
| Page: 1 2 3 |
| Transcriptomic changes along malignancy continuum. |
| 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 |
| 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: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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| Enriched KEGG pathways. |
| 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 |
| 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 |
| VPS39 | SNV | Missense_Mutation | novel | c.487N>A | p.Val163Met | p.V163M | Q96JC1 | protein_coding | deleterious(0.01) | possibly_damaging(0.882) | TCGA-5L-AAT0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| VPS39 | SNV | Missense_Mutation | c.2603C>A | p.Pro868His | p.P868H | Q96JC1 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD | |
| VPS39 | SNV | Missense_Mutation | c.2209G>T | p.Val737Leu | p.V737L | Q96JC1 | protein_coding | deleterious(0.01) | possibly_damaging(0.788) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| VPS39 | SNV | Missense_Mutation | c.670G>A | p.Asp224Asn | p.D224N | Q96JC1 | protein_coding | tolerated(0.32) | benign(0.065) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VPS39 | SNV | Missense_Mutation | novel | c.2194G>T | p.Asp732Tyr | p.D732Y | Q96JC1 | protein_coding | deleterious(0.01) | benign(0.305) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| VPS39 | SNV | Missense_Mutation | c.691N>C | p.Glu231Gln | p.E231Q | Q96JC1 | protein_coding | tolerated(0.54) | possibly_damaging(0.599) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| VPS39 | SNV | Missense_Mutation | novel | c.2140N>G | p.Lys714Glu | p.K714E | Q96JC1 | protein_coding | tolerated(0.15) | benign(0.024) | TCGA-E2-A15E-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| VPS39 | SNV | Missense_Mutation | c.1325N>T | p.Pro442Leu | p.P442L | Q96JC1 | protein_coding | tolerated(0.09) | benign(0.137) | TCGA-E9-A1R3-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | methotrexate | SD | |
| VPS39 | insertion | Nonsense_Mutation | novel | c.1857_1858insTTGGGGTAGT | p.Asn620LeufsTer3 | p.N620Lfs*3 | Q96JC1 | protein_coding | TCGA-AO-A0JJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophospamide | SD | ||
| VPS39 | insertion | Frame_Shift_Ins | novel | c.1856_1857insTTCATCCTGGTGTG | p.Asn620SerfsTer8 | p.N620Sfs*8 | Q96JC1 | protein_coding | TCGA-AO-A0JJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophospamide | SD |
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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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