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Gene: VPS13B |
Gene summary for VPS13B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VPS13B | Gene ID | 157680 |
| Gene name | vacuolar protein sorting 13 homolog B | |
| Gene Alias | CHS1 | |
| Cytomap | 8q22.2 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q7Z7G8 |
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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 |
| 157680 | VPS13B | CCI_1 | Human | Cervix | CC | 4.83e-17 | 1.07e+00 | 0.528 |
| 157680 | VPS13B | CCI_2 | Human | Cervix | CC | 1.55e-16 | 1.71e+00 | 0.5249 |
| 157680 | VPS13B | CCI_3 | Human | Cervix | CC | 4.46e-22 | 1.21e+00 | 0.516 |
| 157680 | VPS13B | CCII_1 | Human | Cervix | CC | 2.08e-06 | 2.63e-01 | 0.3249 |
| 157680 | VPS13B | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.11e-29 | -7.81e-01 | 0.0155 |
| 157680 | VPS13B | HTA11_2487_2000001011 | Human | Colorectum | SER | 7.02e-05 | -4.67e-01 | -0.1808 |
| 157680 | VPS13B | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.18e-06 | -7.96e-01 | 0.0216 |
| 157680 | VPS13B | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.25e-06 | -6.06e-01 | -0.1207 |
| 157680 | VPS13B | HTA11_83_2000001011 | Human | Colorectum | SER | 1.26e-03 | -4.72e-01 | -0.1526 |
| 157680 | VPS13B | HTA11_696_2000001011 | Human | Colorectum | AD | 4.00e-15 | -4.62e-01 | -0.1464 |
| 157680 | VPS13B | HTA11_866_2000001011 | Human | Colorectum | AD | 1.18e-06 | -3.76e-01 | -0.1001 |
| 157680 | VPS13B | HTA11_5212_2000001011 | Human | Colorectum | AD | 3.27e-06 | -7.65e-01 | -0.2061 |
| 157680 | VPS13B | HTA11_9341_2000001011 | Human | Colorectum | SER | 4.87e-02 | -6.30e-01 | -0.00410000000000005 |
| 157680 | VPS13B | HTA11_7862_2000001011 | Human | Colorectum | AD | 1.64e-05 | -6.34e-01 | -0.0179 |
| 157680 | VPS13B | HTA11_866_3004761011 | Human | Colorectum | AD | 3.88e-17 | -6.00e-01 | 0.096 |
| 157680 | VPS13B | HTA11_4255_2000001011 | Human | Colorectum | SER | 1.69e-07 | -6.99e-01 | 0.0446 |
| 157680 | VPS13B | HTA11_9408_2000001011 | Human | Colorectum | AD | 3.82e-04 | -7.94e-01 | 0.0451 |
| 157680 | VPS13B | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.17e-04 | -6.84e-01 | 0.0528 |
| 157680 | VPS13B | HTA11_6801_2000001011 | Human | Colorectum | SER | 9.80e-03 | -7.65e-01 | 0.0171 |
| 157680 | VPS13B | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.22e-04 | -4.59e-01 | 0.0338 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 | ||
| 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. |
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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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| VPS13B | SNV | Missense_Mutation | novel | c.7713N>A | p.Phe2571Leu | p.F2571L | Q7Z7G8 | protein_coding | tolerated(0.13) | probably_damaging(0.97) | TCGA-C8-A8HP-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
| VPS13B | SNV | Missense_Mutation | c.202C>T | p.His68Tyr | p.H68Y | Q7Z7G8 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-C8-A8HQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| VPS13B | SNV | Missense_Mutation | rs752506829 | c.11566N>A | p.Val3856Ile | p.V3856I | Q7Z7G8 | protein_coding | tolerated(0.06) | probably_damaging(0.978) | TCGA-E2-A154-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| VPS13B | SNV | Missense_Mutation | c.11536N>A | p.Asp3846Asn | p.D3846N | Q7Z7G8 | protein_coding | tolerated(0.44) | benign(0.058) | TCGA-E2-A1LH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| VPS13B | SNV | Missense_Mutation | novel | c.7280N>A | p.Arg2427Lys | p.R2427K | Q7Z7G8 | protein_coding | deleterious(0.01) | probably_damaging(0.97) | TCGA-E2-A574-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| VPS13B | SNV | Missense_Mutation | rs781276701 | c.7375A>G | p.Thr2459Ala | p.T2459A | Q7Z7G8 | protein_coding | tolerated(0.07) | benign(0.079) | TCGA-EW-A1J3-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD |
| VPS13B | SNV | Missense_Mutation | novel | c.1703N>T | p.Thr568Ile | p.T568I | Q7Z7G8 | protein_coding | tolerated(0.48) | benign(0) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| VPS13B | insertion | Frame_Shift_Ins | novel | c.10840_10841insATATCCAACAAAGAGTTGGAAGAATACAAGGAAAAATGTTTTA | p.Leu3614HisfsTer21 | p.L3614Hfs*21 | Q7Z7G8 | protein_coding | TCGA-A8-A09C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| VPS13B | insertion | Frame_Shift_Ins | novel | c.4648_4649insGAGAGAGG | p.Asn1550ArgfsTer7 | p.N1550Rfs*7 | Q7Z7G8 | protein_coding | TCGA-AR-A0TU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Doxorubicin | SD | ||
| VPS13B | insertion | Frame_Shift_Ins | novel | c.6713_6714insTTTCC | p.Leu2238PhefsTer17 | p.L2238Ffs*17 | Q7Z7G8 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | 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 42 43 44 45 46 47 48 |
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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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