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Gene: VEPH1 |
Gene summary for VEPH1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VEPH1 | Gene ID | 79674 |
| Gene name | ventricular zone expressed PH domain containing 1 | |
| Gene Alias | MELT | |
| Cytomap | 3q25.31-q25.32 | |
| Gene Type | protein-coding | GO ID | GO:0007154 | UniProtAcc | Q14D04 |
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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 |
| 79674 | VEPH1 | RNA-P10T2-P10T2-2 | Human | Lung | AAH | 2.98e-05 | 5.44e-01 | -0.1406 |
| 79674 | VEPH1 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.79e-13 | 8.26e-01 | -0.2116 |
| 79674 | VEPH1 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 7.95e-10 | 8.16e-01 | -0.1941 |
| 79674 | VEPH1 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 2.55e-08 | 8.28e-01 | -0.2107 |
| 79674 | VEPH1 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 1.29e-17 | 9.52e-01 | -0.2119 |
| 79674 | VEPH1 | RNA-P6T1-P6T1-3 | Human | Lung | MIAC | 4.36e-02 | -2.96e-01 | -0.0296 |
| 79674 | VEPH1 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 1.51e-14 | 2.18e-01 | -0.0166 |
| 79674 | VEPH1 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 6.25e-14 | 1.92e-01 | -0.0132 |
| 79674 | VEPH1 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 5.59e-18 | 1.86e-01 | -0.013 |
| 79674 | VEPH1 | RNA-P6T2-P6T2-4 | Human | Lung | IAC | 5.55e-13 | 3.01e-01 | -0.0121 |
| 79674 | VEPH1 | RNA-P7T1-P7T1-1 | Human | Lung | AIS | 3.51e-04 | 2.62e-02 | -0.0961 |
| 79674 | VEPH1 | RNA-P7T1-P7T1-3 | Human | Lung | AIS | 1.59e-03 | 3.73e-02 | -0.0822 |
| 79674 | VEPH1 | RNA-P7T1-P7T1-4 | Human | Lung | AIS | 2.88e-02 | -1.33e-01 | -0.0809 |
| 79674 | VEPH1 | RNA-P8T2-P8T2-3 | Human | Lung | AIS | 2.26e-04 | 3.84e-01 | -0.1284 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:00715594 | Lung | IAC | response to transforming growth factor beta | 60/2061 | 256/18723 | 9.50e-09 | 1.25e-06 | 60 |
| GO:00715604 | Lung | IAC | cellular response to transforming growth factor beta stimulus | 57/2061 | 250/18723 | 6.17e-08 | 6.54e-06 | 57 |
| GO:00071794 | Lung | IAC | transforming growth factor beta receptor signaling pathway | 45/2061 | 198/18723 | 1.60e-06 | 7.93e-05 | 45 |
| GO:00071785 | Lung | IAC | transmembrane receptor protein serine/threonine kinase signaling pathway | 60/2061 | 355/18723 | 4.82e-04 | 7.03e-03 | 60 |
| GO:19038444 | Lung | IAC | regulation of cellular response to transforming growth factor beta stimulus | 27/2061 | 131/18723 | 9.41e-04 | 1.14e-02 | 27 |
| GO:00170153 | Lung | IAC | regulation of transforming growth factor beta receptor signaling pathway | 26/2061 | 128/18723 | 1.45e-03 | 1.55e-02 | 26 |
| GO:0030512 | Lung | IAC | negative regulation of transforming growth factor beta receptor signaling pathway | 18/2061 | 81/18723 | 2.68e-03 | 2.46e-02 | 18 |
| GO:007155912 | Lung | AIS | response to transforming growth factor beta | 51/1849 | 256/18723 | 8.45e-07 | 6.08e-05 | 51 |
| GO:007156012 | Lung | AIS | cellular response to transforming growth factor beta stimulus | 48/1849 | 250/18723 | 5.13e-06 | 2.47e-04 | 48 |
| GO:000717912 | Lung | AIS | transforming growth factor beta receptor signaling pathway | 39/1849 | 198/18723 | 2.08e-05 | 7.12e-04 | 39 |
| GO:190384412 | Lung | AIS | regulation of cellular response to transforming growth factor beta stimulus | 25/1849 | 131/18723 | 9.61e-04 | 1.27e-02 | 25 |
| GO:000717812 | Lung | AIS | transmembrane receptor protein serine/threonine kinase signaling pathway | 53/1849 | 355/18723 | 1.51e-03 | 1.82e-02 | 53 |
| GO:001701512 | Lung | AIS | regulation of transforming growth factor beta receptor signaling pathway | 24/1849 | 128/18723 | 1.55e-03 | 1.82e-02 | 24 |
| GO:00305121 | Lung | AIS | negative regulation of transforming growth factor beta receptor signaling pathway | 17/1849 | 81/18723 | 2.09e-03 | 2.28e-02 | 17 |
| GO:0090101 | Lung | AIS | negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway | 23/1849 | 131/18723 | 4.54e-03 | 4.00e-02 | 23 |
| GO:007155922 | Lung | MIAC | response to transforming growth factor beta | 28/967 | 256/18723 | 1.51e-04 | 5.95e-03 | 28 |
| GO:007156022 | Lung | MIAC | cellular response to transforming growth factor beta stimulus | 26/967 | 250/18723 | 5.59e-04 | 1.42e-02 | 26 |
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| 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 |
| VEPH1 | SNV | Missense_Mutation | rs373769969 | c.1478N>T | p.Pro493Leu | p.P493L | Q14D04 | protein_coding | deleterious(0.03) | benign(0.048) | TCGA-A2-A04W-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| VEPH1 | SNV | Missense_Mutation | c.2407N>C | p.Asp803His | p.D803H | Q14D04 | protein_coding | deleterious(0) | probably_damaging(0.949) | TCGA-A7-A26G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| VEPH1 | SNV | Missense_Mutation | novel | c.2146N>A | p.Gln716Lys | p.Q716K | Q14D04 | protein_coding | deleterious(0.04) | possibly_damaging(0.791) | TCGA-AC-A8OS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VEPH1 | SNV | Missense_Mutation | novel | c.796N>T | p.Pro266Ser | p.P266S | Q14D04 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VEPH1 | SNV | Missense_Mutation | c.1468N>C | p.Asp490His | p.D490H | Q14D04 | protein_coding | deleterious(0.01) | benign(0.131) | TCGA-AR-A1AO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| VEPH1 | deletion | Frame_Shift_Del | novel | c.2304delN | p.Val769TyrfsTer4 | p.V769Yfs*4 | Q14D04 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| VEPH1 | SNV | Missense_Mutation | c.1557N>C | p.Glu519Asp | p.E519D | Q14D04 | protein_coding | tolerated(0.25) | benign(0.139) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| VEPH1 | SNV | Missense_Mutation | c.625N>G | p.Gln209Glu | p.Q209E | Q14D04 | protein_coding | tolerated(0.2) | benign(0.024) | TCGA-EK-A2R8-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| VEPH1 | SNV | Missense_Mutation | c.79N>A | p.Glu27Lys | p.E27K | Q14D04 | protein_coding | deleterious(0.05) | possibly_damaging(0.907) | TCGA-EK-A2RN-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| VEPH1 | SNV | Missense_Mutation | novel | c.2402N>T | p.Ala801Val | p.A801V | Q14D04 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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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