|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: VPS51 |
Gene summary for VPS51 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VPS51 | Gene ID | 738 |
| Gene name | VPS51 subunit of GARP complex | |
| Gene Alias | ANG2 | |
| Cytomap | 11q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9UID3 |
Top |
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 |
| 738 | VPS51 | C30 | Human | Oral cavity | OSCC | 6.96e-09 | 6.96e-01 | 0.3055 |
| 738 | VPS51 | C43 | Human | Oral cavity | OSCC | 1.13e-27 | 7.19e-01 | 0.1704 |
| 738 | VPS51 | C46 | Human | Oral cavity | OSCC | 1.24e-36 | 9.53e-01 | 0.1673 |
| 738 | VPS51 | C51 | Human | Oral cavity | OSCC | 9.36e-06 | 5.70e-01 | 0.2674 |
| 738 | VPS51 | C57 | Human | Oral cavity | OSCC | 5.38e-11 | 5.02e-01 | 0.1679 |
| 738 | VPS51 | C06 | Human | Oral cavity | OSCC | 3.78e-04 | 1.05e+00 | 0.2699 |
| 738 | VPS51 | C08 | Human | Oral cavity | OSCC | 2.30e-35 | 8.59e-01 | 0.1919 |
| 738 | VPS51 | C09 | Human | Oral cavity | OSCC | 4.00e-05 | 3.02e-01 | 0.1431 |
| 738 | VPS51 | LN46 | Human | Oral cavity | OSCC | 9.07e-19 | 9.53e-01 | 0.1666 |
| 738 | VPS51 | LP15 | Human | Oral cavity | LP | 2.30e-06 | 1.30e+00 | 0.2174 |
| 738 | VPS51 | LP17 | Human | Oral cavity | LP | 8.93e-06 | 8.57e-01 | 0.2349 |
| 738 | VPS51 | SYSMH1 | Human | Oral cavity | OSCC | 2.95e-19 | 5.98e-01 | 0.1127 |
| 738 | VPS51 | SYSMH2 | Human | Oral cavity | OSCC | 7.65e-22 | 7.99e-01 | 0.2326 |
| 738 | VPS51 | SYSMH3 | Human | Oral cavity | OSCC | 1.38e-25 | 7.63e-01 | 0.2442 |
| 738 | VPS51 | SYSMH4 | Human | Oral cavity | OSCC | 6.63e-06 | 2.20e-01 | 0.1226 |
| 738 | VPS51 | SYSMH5 | Human | Oral cavity | OSCC | 1.60e-14 | 6.02e-01 | 0.0647 |
| 738 | VPS51 | SYSMH6 | Human | Oral cavity | OSCC | 2.27e-15 | 4.85e-01 | 0.1275 |
| 738 | VPS51 | P2_S3_AK | Human | Skin | AK | 3.55e-02 | 1.57e-01 | -0.3287 |
| 738 | VPS51 | P4_S8_cSCC | Human | Skin | cSCC | 5.00e-11 | 3.02e-01 | -0.3095 |
| 738 | VPS51 | P1_cSCC | Human | Skin | cSCC | 1.71e-31 | 1.03e+00 | 0.0292 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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. |
Top |
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:004819317 | Esophagus | HGIN | Golgi vesicle transport | 83/2587 | 296/18723 | 8.59e-11 | 8.89e-09 | 83 |
| GO:001619710 | Esophagus | HGIN | endosomal transport | 57/2587 | 230/18723 | 5.74e-06 | 1.81e-04 | 57 |
| GO:009887610 | Esophagus | HGIN | vesicle-mediated transport to the plasma membrane | 36/2587 | 136/18723 | 6.76e-05 | 1.55e-03 | 36 |
| GO:000703416 | Esophagus | HGIN | vacuolar transport | 35/2587 | 157/18723 | 2.52e-03 | 2.51e-02 | 35 |
| GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| 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:001648210 | Esophagus | ESCC | cytosolic transport | 124/8552 | 168/18723 | 9.69e-14 | 4.69e-12 | 124 |
| 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:00070308 | Esophagus | ESCC | Golgi organization | 101/8552 | 157/18723 | 1.78e-06 | 2.10e-05 | 101 |
| GO:00421477 | Esophagus | ESCC | retrograde transport, endosome to Golgi | 63/8552 | 91/18723 | 4.58e-06 | 4.87e-05 | 63 |
| GO:00324565 | Esophagus | ESCC | endocytic recycling | 51/8552 | 73/18723 | 2.47e-05 | 2.10e-04 | 51 |
| GO:004819311 | Liver | Cirrhotic | Golgi vesicle transport | 153/4634 | 296/18723 | 1.02e-23 | 6.43e-21 | 153 |
| GO:000703411 | Liver | Cirrhotic | vacuolar transport | 75/4634 | 157/18723 | 3.13e-10 | 1.53e-08 | 75 |
| GO:001648211 | Liver | Cirrhotic | cytosolic transport | 74/4634 | 168/18723 | 3.34e-08 | 1.12e-06 | 74 |
| GO:001619711 | Liver | Cirrhotic | endosomal transport | 93/4634 | 230/18723 | 1.01e-07 | 2.93e-06 | 93 |
| GO:00070301 | Liver | Cirrhotic | Golgi organization | 68/4634 | 157/18723 | 2.57e-07 | 6.41e-06 | 68 |
| GO:009887611 | Liver | Cirrhotic | vesicle-mediated transport to the plasma membrane | 59/4634 | 136/18723 | 1.46e-06 | 2.88e-05 | 59 |
| GO:000704111 | Liver | Cirrhotic | lysosomal transport | 50/4634 | 114/18723 | 6.15e-06 | 9.82e-05 | 50 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| VPS51 | SNV | Missense_Mutation | rs375386887 | c.1721N>A | p.Arg574Gln | p.R574Q | Q9UID3 | protein_coding | tolerated(0.48) | benign(0.014) | TCGA-B6-A409-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
| VPS51 | SNV | Missense_Mutation | rs144624856 | c.1717C>T | p.Arg573Trp | p.R573W | Q9UID3 | protein_coding | deleterious(0) | possibly_damaging(0.613) | TCGA-BH-A5J0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| VPS51 | insertion | Frame_Shift_Ins | novel | c.429_430insAATGTGTATATGT | p.Ala144AsnfsTer43 | p.A144Nfs*43 | Q9UID3 | protein_coding | TCGA-AN-A03Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| VPS51 | SNV | Missense_Mutation | rs377434441 | c.307N>A | p.Asp103Asn | p.D103N | Q9UID3 | protein_coding | tolerated(0.06) | probably_damaging(0.97) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| VPS51 | SNV | Missense_Mutation | c.315N>C | p.Gln105His | p.Q105H | Q9UID3 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| VPS51 | SNV | Missense_Mutation | novel | c.288N>T | p.Gln96His | p.Q96H | Q9UID3 | protein_coding | tolerated(0.06) | probably_damaging(0.945) | TCGA-VS-A94X-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| VPS51 | SNV | Missense_Mutation | c.412N>T | p.Arg138Trp | p.R138W | Q9UID3 | protein_coding | tolerated(0.09) | possibly_damaging(0.903) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| VPS51 | SNV | Missense_Mutation | c.1749G>T | p.Gln583His | p.Q583H | Q9UID3 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| VPS51 | SNV | Missense_Mutation | rs780357113 | c.1873G>A | p.Val625Met | p.V625M | Q9UID3 | protein_coding | tolerated(0.18) | possibly_damaging(0.808) | TCGA-DM-A28A-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| VPS51 | SNV | Missense_Mutation | c.934G>T | p.Val312Leu | p.V312L | Q9UID3 | protein_coding | tolerated(1) | benign(0.013) | TCGA-G4-6586-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |