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Gene: VMP1 |
Gene summary for VMP1 |
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Gene information | Species | Human | Gene symbol | VMP1 | Gene ID | 81671 |
Gene name | vacuole membrane protein 1 | |
Gene Alias | EPG3 | |
Cytomap | 17q23.1 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q96GC9 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
81671 | VMP1 | TD9 | Human | Lung | IAC | 1.67e-08 | 9.41e-01 | 0.088 |
81671 | VMP1 | RNA-P10T2-P10T2-2 | Human | Lung | AAH | 5.10e-05 | 1.08e+00 | -0.1406 |
81671 | VMP1 | RNA-P10T2-P10T2-3 | Human | Lung | AAH | 2.54e-02 | 9.95e-01 | -0.1408 |
81671 | VMP1 | RNA-P10T2-P10T2-4 | Human | Lung | AAH | 1.34e-03 | 1.13e+00 | -0.138 |
81671 | VMP1 | RNA-P17T-P17T-2 | Human | Lung | IAC | 3.63e-08 | 1.11e+00 | 0.3371 |
81671 | VMP1 | RNA-P17T-P17T-4 | Human | Lung | IAC | 3.69e-13 | 1.15e+00 | 0.343 |
81671 | VMP1 | RNA-P17T-P17T-6 | Human | Lung | IAC | 1.79e-09 | 1.17e+00 | 0.3385 |
81671 | VMP1 | RNA-P17T-P17T-8 | Human | Lung | IAC | 5.87e-10 | 1.11e+00 | 0.3329 |
81671 | VMP1 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 4.63e-07 | 4.00e-01 | -0.2116 |
81671 | VMP1 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 8.33e-05 | 3.85e-01 | -0.2107 |
81671 | VMP1 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 1.49e-09 | 4.45e-01 | -0.2119 |
81671 | VMP1 | RNA-P3T-P3T-1 | Human | Lung | IAC | 2.12e-12 | 9.93e-01 | 0.1829 |
81671 | VMP1 | RNA-P3T-P3T-2 | Human | Lung | IAC | 1.12e-08 | 8.53e-01 | 0.1835 |
81671 | VMP1 | RNA-P3T-P3T-4 | Human | Lung | IAC | 1.02e-10 | 8.85e-01 | 0.1859 |
81671 | VMP1 | RNA-P6T1-P6T1-1 | Human | Lung | MIAC | 2.27e-04 | 9.59e-01 | -0.0238 |
81671 | VMP1 | RNA-P6T1-P6T1-3 | Human | Lung | MIAC | 1.81e-02 | 5.52e-01 | -0.0296 |
81671 | VMP1 | RNA-P6T1-P6T1-4 | Human | Lung | MIAC | 2.41e-04 | 8.09e-01 | -0.0263 |
81671 | VMP1 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 6.94e-37 | 1.02e+00 | -0.0166 |
81671 | VMP1 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 2.23e-40 | 1.01e+00 | -0.0132 |
81671 | VMP1 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 1.59e-40 | 9.51e-01 | -0.013 |
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∗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 |
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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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00075653 | Breast | Precancer | female pregnancy | 29/1080 | 193/18723 | 2.07e-06 | 7.31e-05 | 29 |
GO:00447063 | Breast | Precancer | multi-multicellular organism process | 31/1080 | 220/18723 | 3.73e-06 | 1.19e-04 | 31 |
GO:00075663 | Breast | Precancer | embryo implantation | 11/1080 | 53/18723 | 1.82e-04 | 2.95e-03 | 11 |
GO:00224119 | Breast | Precancer | cellular component disassembly | 44/1080 | 443/18723 | 3.17e-04 | 4.51e-03 | 44 |
GO:00324116 | Breast | Precancer | positive regulation of transporter activity | 16/1080 | 120/18723 | 1.46e-03 | 1.51e-02 | 16 |
GO:00347673 | Breast | Precancer | positive regulation of ion transmembrane transport | 19/1080 | 167/18723 | 3.60e-03 | 2.98e-02 | 19 |
GO:00324143 | Breast | Precancer | positive regulation of ion transmembrane transporter activity | 14/1080 | 109/18723 | 3.97e-03 | 3.15e-02 | 14 |
GO:00109596 | Breast | Precancer | regulation of metal ion transport | 37/1080 | 406/18723 | 4.07e-03 | 3.22e-02 | 37 |
GO:00228985 | Breast | Precancer | regulation of transmembrane transporter activity | 27/1080 | 278/18723 | 5.72e-03 | 4.11e-02 | 27 |
GO:1901021 | Breast | Precancer | positive regulation of calcium ion transmembrane transporter activity | 7/1080 | 39/18723 | 6.32e-03 | 4.43e-02 | 7 |
GO:1901019 | Breast | Precancer | regulation of calcium ion transmembrane transporter activity | 12/1080 | 93/18723 | 7.09e-03 | 4.78e-02 | 12 |
GO:000756511 | Breast | IDC | female pregnancy | 39/1434 | 193/18723 | 1.81e-08 | 1.27e-06 | 39 |
GO:00447061 | Breast | IDC | multi-multicellular organism process | 41/1434 | 220/18723 | 8.58e-08 | 5.19e-06 | 41 |
GO:000756611 | Breast | IDC | embryo implantation | 14/1434 | 53/18723 | 3.14e-05 | 7.32e-04 | 14 |
GO:001095913 | Breast | IDC | regulation of metal ion transport | 52/1434 | 406/18723 | 1.76e-04 | 2.97e-03 | 52 |
GO:003241111 | Breast | IDC | positive regulation of transporter activity | 20/1434 | 120/18723 | 7.64e-04 | 9.27e-03 | 20 |
GO:00432703 | Breast | IDC | positive regulation of ion transport | 36/1434 | 275/18723 | 1.11e-03 | 1.22e-02 | 36 |
GO:002289812 | Breast | IDC | regulation of transmembrane transporter activity | 36/1434 | 278/18723 | 1.35e-03 | 1.40e-02 | 36 |
GO:003241411 | Breast | IDC | positive regulation of ion transmembrane transporter activity | 18/1434 | 109/18723 | 1.53e-03 | 1.53e-02 | 18 |
GO:003476711 | Breast | IDC | positive regulation of ion transmembrane transport | 24/1434 | 167/18723 | 2.07e-03 | 1.95e-02 | 24 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04140 | Colorectum | AD | Autophagy - animal | 49/2092 | 141/8465 | 4.58e-03 | 2.20e-02 | 1.40e-02 | 49 |
hsa041401 | Colorectum | AD | Autophagy - animal | 49/2092 | 141/8465 | 4.58e-03 | 2.20e-02 | 1.40e-02 | 49 |
hsa041402 | Colorectum | SER | Autophagy - animal | 39/1580 | 141/8465 | 5.43e-03 | 3.28e-02 | 2.38e-02 | 39 |
hsa041403 | Colorectum | SER | Autophagy - animal | 39/1580 | 141/8465 | 5.43e-03 | 3.28e-02 | 2.38e-02 | 39 |
hsa041404 | Colorectum | MSS | Autophagy - animal | 45/1875 | 141/8465 | 4.42e-03 | 1.90e-02 | 1.16e-02 | 45 |
hsa041405 | Colorectum | MSS | Autophagy - animal | 45/1875 | 141/8465 | 4.42e-03 | 1.90e-02 | 1.16e-02 | 45 |
hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
hsa041406 | Liver | Cirrhotic | Autophagy - animal | 65/2530 | 141/8465 | 3.10e-05 | 2.47e-04 | 1.52e-04 | 65 |
hsa0414011 | Liver | Cirrhotic | Autophagy - animal | 65/2530 | 141/8465 | 3.10e-05 | 2.47e-04 | 1.52e-04 | 65 |
hsa0414021 | Liver | HCC | Autophagy - animal | 99/4020 | 141/8465 | 3.08e-08 | 4.70e-07 | 2.61e-07 | 99 |
hsa0414031 | Liver | HCC | Autophagy - animal | 99/4020 | 141/8465 | 3.08e-08 | 4.70e-07 | 2.61e-07 | 99 |
hsa041407 | Lung | IAC | Autophagy - animal | 28/1053 | 141/8465 | 7.64e-03 | 3.03e-02 | 2.01e-02 | 28 |
hsa0414012 | Lung | IAC | Autophagy - animal | 28/1053 | 141/8465 | 7.64e-03 | 3.03e-02 | 2.01e-02 | 28 |
hsa041409 | Oral cavity | OSCC | Autophagy - animal | 94/3704 | 141/8465 | 2.73e-08 | 2.38e-07 | 1.21e-07 | 94 |
hsa0414014 | Oral cavity | OSCC | Autophagy - animal | 94/3704 | 141/8465 | 2.73e-08 | 2.38e-07 | 1.21e-07 | 94 |
hsa0414024 | Oral cavity | LP | Autophagy - animal | 55/2418 | 141/8465 | 4.54e-03 | 1.87e-02 | 1.20e-02 | 55 |
hsa0414034 | Oral cavity | LP | Autophagy - animal | 55/2418 | 141/8465 | 4.54e-03 | 1.87e-02 | 1.20e-02 | 55 |
hsa0414041 | Oral cavity | EOLP | Autophagy - animal | 39/1218 | 141/8465 | 2.68e-05 | 1.38e-04 | 8.12e-05 | 39 |
hsa0414051 | Oral cavity | EOLP | Autophagy - animal | 39/1218 | 141/8465 | 2.68e-05 | 1.38e-04 | 8.12e-05 | 39 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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. |
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Somatic mutation of malignant transformation related genes |
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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 |
VMP1 | SNV | Missense_Mutation | c.1181N>A | p.Arg394Gln | p.R394Q | Q96GC9 | protein_coding | deleterious(0) | benign(0.288) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
VMP1 | insertion | Frame_Shift_Ins | novel | c.577_578insCAGGGGGT | p.Met193ThrfsTer62 | p.M193Tfs*62 | Q96GC9 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
VMP1 | deletion | Frame_Shift_Del | novel | c.248delT | p.Leu83TyrfsTer8 | p.L83Yfs*8 | Q96GC9 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
VMP1 | SNV | Missense_Mutation | c.669G>C | p.Glu223Asp | p.E223D | Q96GC9 | protein_coding | tolerated(0.69) | benign(0.012) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
VMP1 | SNV | Missense_Mutation | c.1048N>T | p.His350Tyr | p.H350Y | Q96GC9 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-FU-A40J-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | carboplatin | CR | |
VMP1 | SNV | Missense_Mutation | novel | c.814G>C | p.Asp272His | p.D272H | Q96GC9 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
VMP1 | SNV | Missense_Mutation | c.1036N>T | p.Arg346Trp | p.R346W | Q96GC9 | protein_coding | deleterious(0) | possibly_damaging(0.828) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
VMP1 | SNV | Missense_Mutation | c.601G>A | p.Gly201Arg | p.G201R | Q96GC9 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VMP1 | SNV | Missense_Mutation | novel | c.131N>G | p.Ile44Ser | p.I44S | Q96GC9 | protein_coding | deleterious(0) | possibly_damaging(0.767) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VMP1 | SNV | Missense_Mutation | c.926N>C | p.Ile309Thr | p.I309T | Q96GC9 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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