|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: VPS13D |
Gene summary for VPS13D |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VPS13D | Gene ID | 55187 |
| Gene name | vacuolar protein sorting 13 homolog D | |
| Gene Alias | SCAR4 | |
| Cytomap | 1p36.22-p36.21 | |
| Gene Type | protein-coding | GO ID | GO:0000422 | UniProtAcc | Q5THJ4 |
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 |
| 55187 | VPS13D | CCI_1 | Human | Cervix | CC | 1.79e-08 | 1.46e+00 | 0.528 |
| 55187 | VPS13D | CCI_2 | Human | Cervix | CC | 2.47e-11 | 1.07e+00 | 0.5249 |
| 55187 | VPS13D | CCI_3 | Human | Cervix | CC | 1.99e-20 | 1.32e+00 | 0.516 |
| 55187 | VPS13D | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.02e-24 | -4.84e-01 | 0.0155 |
| 55187 | VPS13D | HTA11_347_2000001011 | Human | Colorectum | AD | 2.51e-05 | 5.16e-01 | -0.1954 |
| 55187 | VPS13D | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.14e-02 | -3.66e-01 | 0.0446 |
| 55187 | VPS13D | HTA11_11156_2000001011 | Human | Colorectum | AD | 1.87e-02 | -8.10e-01 | 0.0397 |
| 55187 | VPS13D | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.41e-03 | -4.97e-01 | 0.0588 |
| 55187 | VPS13D | HTA11_99999973899_84307 | Human | Colorectum | MSS | 9.25e-04 | -4.11e-01 | 0.2585 |
| 55187 | VPS13D | HTA11_99999974143_84620 | Human | Colorectum | MSS | 5.68e-19 | -6.11e-01 | 0.3005 |
| 55187 | VPS13D | F007 | Human | Colorectum | FAP | 4.77e-09 | -4.50e-01 | 0.1176 |
| 55187 | VPS13D | A002-C-010 | Human | Colorectum | FAP | 1.81e-02 | -2.91e-01 | 0.242 |
| 55187 | VPS13D | A001-C-207 | Human | Colorectum | FAP | 4.47e-09 | -4.06e-01 | 0.1278 |
| 55187 | VPS13D | A015-C-203 | Human | Colorectum | FAP | 1.86e-35 | -5.44e-01 | -0.1294 |
| 55187 | VPS13D | A015-C-204 | Human | Colorectum | FAP | 3.34e-08 | -2.34e-01 | -0.0228 |
| 55187 | VPS13D | A014-C-040 | Human | Colorectum | FAP | 3.00e-06 | -3.10e-01 | -0.1184 |
| 55187 | VPS13D | A002-C-201 | Human | Colorectum | FAP | 3.80e-24 | -4.59e-01 | 0.0324 |
| 55187 | VPS13D | A002-C-203 | Human | Colorectum | FAP | 5.36e-05 | -2.81e-01 | 0.2786 |
| 55187 | VPS13D | A001-C-119 | Human | Colorectum | FAP | 2.76e-13 | -3.96e-01 | -0.1557 |
| 55187 | VPS13D | A001-C-108 | Human | Colorectum | FAP | 1.14e-16 | -2.72e-01 | -0.0272 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00725949 | Cervix | CC | establishment of protein localization to organelle | 99/2311 | 422/18723 | 1.23e-10 | 2.11e-08 | 99 |
| GO:000989610 | Cervix | CC | positive regulation of catabolic process | 109/2311 | 492/18723 | 5.26e-10 | 6.99e-08 | 109 |
| GO:00512359 | Cervix | CC | maintenance of location | 78/2311 | 327/18723 | 5.18e-09 | 4.92e-07 | 78 |
| GO:005165110 | Cervix | CC | maintenance of location in cell | 55/2311 | 214/18723 | 6.63e-08 | 3.85e-06 | 55 |
| GO:003133110 | Cervix | CC | positive regulation of cellular catabolic process | 91/2311 | 427/18723 | 9.64e-08 | 5.25e-06 | 91 |
| GO:000660510 | Cervix | CC | protein targeting | 68/2311 | 314/18723 | 2.17e-06 | 6.55e-05 | 68 |
| GO:00325077 | Cervix | CC | maintenance of protein location in cell | 21/2311 | 65/18723 | 2.03e-05 | 3.71e-04 | 21 |
| GO:004518510 | Cervix | CC | maintenance of protein location | 26/2311 | 94/18723 | 4.85e-05 | 7.34e-04 | 26 |
| GO:002241110 | Cervix | CC | cellular component disassembly | 83/2311 | 443/18723 | 6.04e-05 | 8.68e-04 | 83 |
| GO:00726655 | Cervix | CC | protein localization to vacuole | 20/2311 | 67/18723 | 1.12e-04 | 1.40e-03 | 20 |
| GO:00108218 | Cervix | CC | regulation of mitochondrion organization | 34/2311 | 144/18723 | 1.27e-04 | 1.58e-03 | 34 |
| GO:00162367 | Cervix | CC | macroautophagy | 58/2311 | 291/18723 | 1.40e-04 | 1.70e-03 | 58 |
| GO:00105067 | Cervix | CC | regulation of autophagy | 61/2311 | 317/18723 | 2.61e-04 | 2.87e-03 | 61 |
| GO:00004227 | Cervix | CC | autophagy of mitochondrion | 21/2311 | 81/18723 | 6.47e-04 | 6.02e-03 | 21 |
| GO:00617267 | Cervix | CC | mitochondrion disassembly | 21/2311 | 81/18723 | 6.47e-04 | 6.02e-03 | 21 |
| GO:00070347 | Cervix | CC | vacuolar transport | 34/2311 | 157/18723 | 7.03e-04 | 6.40e-03 | 34 |
| GO:00066235 | Cervix | CC | protein targeting to vacuole | 12/2311 | 37/18723 | 1.15e-03 | 9.39e-03 | 12 |
| GO:00108224 | Cervix | CC | positive regulation of mitochondrion organization | 19/2311 | 74/18723 | 1.30e-03 | 1.03e-02 | 19 |
| GO:00726665 | Cervix | CC | establishment of protein localization to vacuole | 14/2311 | 49/18723 | 1.84e-03 | 1.37e-02 | 14 |
| GO:19031466 | Cervix | CC | regulation of autophagy of mitochondrion | 10/2311 | 33/18723 | 5.07e-03 | 3.00e-02 | 10 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| 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 |
| VPS13D | SNV | Missense_Mutation | c.5552N>C | p.Ile1851Thr | p.I1851T | Q5THJ4 | protein_coding | tolerated(0.59) | benign(0) | TCGA-A1-A0SO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | SD | ||
| VPS13D | SNV | Missense_Mutation | c.11399N>A | p.Ser3800Asn | p.S3800N | Q5THJ4 | protein_coding | tolerated(0.71) | benign(0) | TCGA-A2-A0CS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD | |
| VPS13D | SNV | Missense_Mutation | novel | c.3030N>C | p.Gln1010His | p.Q1010H | Q5THJ4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A7-A6VX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR |
| VPS13D | SNV | Missense_Mutation | rs763271218 | c.7067C>T | p.Thr2356Met | p.T2356M | Q5THJ4 | protein_coding | tolerated(0.08) | benign(0.322) | TCGA-A8-A08P-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
| VPS13D | SNV | Missense_Mutation | c.9985G>C | p.Glu3329Gln | p.E3329Q | Q5THJ4 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VPS13D | SNV | Missense_Mutation | rs771180052 | c.3561G>T | p.Glu1187Asp | p.E1187D | Q5THJ4 | protein_coding | tolerated(0.17) | benign(0.007) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VPS13D | SNV | Missense_Mutation | novel | c.4298C>A | p.Ser1433Tyr | p.S1433Y | Q5THJ4 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VPS13D | SNV | Missense_Mutation | c.5452N>A | p.Asp1818Asn | p.D1818N | Q5THJ4 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| VPS13D | SNV | Missense_Mutation | c.8179G>C | p.Ala2727Pro | p.A2727P | Q5THJ4 | protein_coding | deleterious(0.02) | probably_damaging(0.972) | TCGA-AR-A24P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| VPS13D | SNV | Missense_Mutation | rs775755003 | c.913N>G | p.Trp305Gly | p.W305G | Q5THJ4 | protein_coding | tolerated(0.17) | benign(0.169) | TCGA-BH-A0AW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD |
| 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 38 39 40 41 |
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 |