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Gene: VAMP2 |
Gene summary for VAMP2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | VAMP2 | Gene ID | 6844 |
Gene name | vesicle associated membrane protein 2 | |
Gene Alias | NEDHAHM | |
Cytomap | 17p13.1 | |
Gene Type | protein-coding | GO ID | GO:0001505 | UniProtAcc | F8WCA0 |
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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 |
6844 | VAMP2 | GSM4909320 | Human | Breast | IDC | 1.69e-12 | -3.12e-01 | 0.1575 |
6844 | VAMP2 | GSM4909321 | Human | Breast | IDC | 3.23e-18 | -2.02e-01 | 0.1559 |
6844 | VAMP2 | M2 | Human | Breast | IDC | 6.35e-03 | -4.35e-01 | 0.21 |
6844 | VAMP2 | NCCBC14 | Human | Breast | DCIS | 3.48e-25 | -5.04e-01 | 0.2021 |
6844 | VAMP2 | NCCBC2 | Human | Breast | DCIS | 5.05e-05 | -5.37e-01 | 0.1554 |
6844 | VAMP2 | NCCBC5 | Human | Breast | DCIS | 7.12e-22 | -4.36e-01 | 0.2046 |
6844 | VAMP2 | P1 | Human | Breast | IDC | 1.71e-29 | -4.10e-01 | 0.1527 |
6844 | VAMP2 | P2 | Human | Breast | IDC | 2.29e-11 | -3.73e-01 | 0.21 |
6844 | VAMP2 | DCIS2 | Human | Breast | DCIS | 1.03e-43 | 2.42e-01 | 0.0085 |
6844 | VAMP2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.02e-11 | 2.27e-01 | 0.0155 |
6844 | VAMP2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.43e-18 | 4.77e-01 | -0.1808 |
6844 | VAMP2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.22e-05 | 3.36e-01 | 0.0216 |
6844 | VAMP2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.77e-18 | 4.99e-01 | -0.0811 |
6844 | VAMP2 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.65e-10 | 3.19e-01 | -0.1088 |
6844 | VAMP2 | HTA11_347_2000001011 | Human | Colorectum | AD | 7.01e-30 | 5.54e-01 | -0.1954 |
6844 | VAMP2 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.50e-11 | 6.61e-01 | -0.2602 |
6844 | VAMP2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.29e-05 | 4.53e-01 | -0.2196 |
6844 | VAMP2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.02e-14 | 3.79e-01 | -0.1207 |
6844 | VAMP2 | HTA11_83_2000001011 | Human | Colorectum | SER | 8.95e-14 | 4.31e-01 | -0.1526 |
6844 | VAMP2 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.84e-22 | 4.18e-01 | -0.1464 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:003428414 | Breast | IDC | response to monosaccharide | 36/1434 | 225/18723 | 1.94e-05 | 4.83e-04 | 36 |
GO:000974314 | Breast | IDC | response to carbohydrate | 38/1434 | 253/18723 | 4.87e-05 | 1.07e-03 | 38 |
GO:190495113 | Breast | IDC | positive regulation of establishment of protein localization | 45/1434 | 319/18723 | 5.01e-05 | 1.09e-03 | 45 |
GO:00434348 | Breast | IDC | response to peptide hormone | 54/1434 | 414/18723 | 8.25e-05 | 1.61e-03 | 54 |
GO:000974613 | Breast | IDC | response to hexose | 33/1434 | 219/18723 | 1.39e-04 | 2.49e-03 | 33 |
GO:001095913 | Breast | IDC | regulation of metal ion transport | 52/1434 | 406/18723 | 1.76e-04 | 2.97e-03 | 52 |
GO:000974913 | Breast | IDC | response to glucose | 31/1434 | 212/18723 | 3.75e-04 | 5.35e-03 | 31 |
GO:005122213 | Breast | IDC | positive regulation of protein transport | 40/1434 | 303/18723 | 5.14e-04 | 6.70e-03 | 40 |
GO:002289812 | Breast | IDC | regulation of transmembrane transporter activity | 36/1434 | 278/18723 | 1.35e-03 | 1.40e-02 | 36 |
GO:00324125 | Breast | IDC | regulation of ion transmembrane transporter activity | 33/1434 | 267/18723 | 4.38e-03 | 3.40e-02 | 33 |
GO:00324096 | Breast | IDC | regulation of transporter activity | 37/1434 | 310/18723 | 4.77e-03 | 3.66e-02 | 37 |
GO:00331578 | Breast | IDC | regulation of intracellular protein transport | 29/1434 | 229/18723 | 5.16e-03 | 3.84e-02 | 29 |
GO:00726599 | Breast | IDC | protein localization to plasma membrane | 34/1434 | 284/18723 | 6.33e-03 | 4.47e-02 | 34 |
GO:00323888 | Breast | IDC | positive regulation of intracellular transport | 26/1434 | 202/18723 | 6.33e-03 | 4.47e-02 | 26 |
GO:00328687 | Breast | IDC | response to insulin | 32/1434 | 264/18723 | 6.61e-03 | 4.62e-02 | 32 |
GO:00328697 | Breast | IDC | cellular response to insulin stimulus | 26/1434 | 203/18723 | 6.74e-03 | 4.68e-02 | 26 |
GO:003428424 | Breast | DCIS | response to monosaccharide | 36/1390 | 225/18723 | 9.86e-06 | 2.60e-04 | 36 |
GO:190495123 | Breast | DCIS | positive regulation of establishment of protein localization | 45/1390 | 319/18723 | 2.36e-05 | 5.52e-04 | 45 |
GO:000974324 | Breast | DCIS | response to carbohydrate | 38/1390 | 253/18723 | 2.48e-05 | 5.72e-04 | 38 |
GO:000974623 | Breast | DCIS | response to hexose | 33/1390 | 219/18723 | 7.73e-05 | 1.48e-03 | 33 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa049704 | Breast | IDC | Salivary secretion | 18/867 | 93/8465 | 5.69e-03 | 3.13e-02 | 2.34e-02 | 18 |
hsa0497011 | Breast | IDC | Salivary secretion | 18/867 | 93/8465 | 5.69e-03 | 3.13e-02 | 2.34e-02 | 18 |
hsa04962 | Colorectum | AD | Vasopressin-regulated water reabsorption | 19/2092 | 44/8465 | 5.48e-03 | 2.48e-02 | 1.58e-02 | 19 |
hsa049621 | Colorectum | AD | Vasopressin-regulated water reabsorption | 19/2092 | 44/8465 | 5.48e-03 | 2.48e-02 | 1.58e-02 | 19 |
hsa049622 | Colorectum | MSS | Vasopressin-regulated water reabsorption | 17/1875 | 44/8465 | 9.76e-03 | 3.55e-02 | 2.18e-02 | 17 |
hsa049623 | Colorectum | MSS | Vasopressin-regulated water reabsorption | 17/1875 | 44/8465 | 9.76e-03 | 3.55e-02 | 2.18e-02 | 17 |
hsa049627 | Esophagus | HGIN | Vasopressin-regulated water reabsorption | 14/1383 | 44/8465 | 8.21e-03 | 4.71e-02 | 3.74e-02 | 14 |
hsa0496214 | Esophagus | HGIN | Vasopressin-regulated water reabsorption | 14/1383 | 44/8465 | 8.21e-03 | 4.71e-02 | 3.74e-02 | 14 |
hsa041305 | Esophagus | ESCC | SNARE interactions in vesicular transport | 28/4205 | 33/8465 | 2.75e-05 | 1.32e-04 | 6.75e-05 | 28 |
hsa0496223 | Esophagus | ESCC | Vasopressin-regulated water reabsorption | 33/4205 | 44/8465 | 5.27e-04 | 1.78e-03 | 9.13e-04 | 33 |
hsa0413012 | Esophagus | ESCC | SNARE interactions in vesicular transport | 28/4205 | 33/8465 | 2.75e-05 | 1.32e-04 | 6.75e-05 | 28 |
hsa0496233 | Esophagus | ESCC | Vasopressin-regulated water reabsorption | 33/4205 | 44/8465 | 5.27e-04 | 1.78e-03 | 9.13e-04 | 33 |
hsa04130 | Liver | Cirrhotic | SNARE interactions in vesicular transport | 18/2530 | 33/8465 | 2.64e-03 | 1.10e-02 | 6.76e-03 | 18 |
hsa041301 | Liver | Cirrhotic | SNARE interactions in vesicular transport | 18/2530 | 33/8465 | 2.64e-03 | 1.10e-02 | 6.76e-03 | 18 |
hsa041302 | Liver | HCC | SNARE interactions in vesicular transport | 25/4020 | 33/8465 | 8.78e-04 | 3.38e-03 | 1.88e-03 | 25 |
hsa041303 | Liver | HCC | SNARE interactions in vesicular transport | 25/4020 | 33/8465 | 8.78e-04 | 3.38e-03 | 1.88e-03 | 25 |
hsa041304 | Oral cavity | OSCC | SNARE interactions in vesicular transport | 28/3704 | 33/8465 | 1.31e-06 | 7.18e-06 | 3.66e-06 | 28 |
hsa049626 | Oral cavity | OSCC | Vasopressin-regulated water reabsorption | 29/3704 | 44/8465 | 2.47e-03 | 6.52e-03 | 3.32e-03 | 29 |
hsa0413011 | Oral cavity | OSCC | SNARE interactions in vesicular transport | 28/3704 | 33/8465 | 1.31e-06 | 7.18e-06 | 3.66e-06 | 28 |
hsa0496213 | Oral cavity | OSCC | Vasopressin-regulated water reabsorption | 29/3704 | 44/8465 | 2.47e-03 | 6.52e-03 | 3.32e-03 | 29 |
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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 |
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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. |
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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 |
VAMP2 | SNV | Missense_Mutation | c.175N>A | p.Asp59Asn | p.D59N | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | ||
VAMP2 | SNV | Missense_Mutation | novel | c.96G>T | p.Arg32Ser | p.R32S | protein_coding | deleterious(0) | benign(0.248) | TCGA-B5-A1MX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Hormone Therapy | megace | SD | |
VAMP2 | SNV | Missense_Mutation | novel | c.136N>A | p.Asp46Asn | p.D46N | protein_coding | deleterious(0.02) | benign(0.135) | TCGA-DF-A2KN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD | |
VAMP2 | SNV | Missense_Mutation | novel | c.95N>T | p.Arg32Met | p.R32M | protein_coding | deleterious(0) | possibly_damaging(0.746) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
VAMP2 | SNV | Missense_Mutation | novel | c.28N>C | p.Ala10Pro | p.A10P | protein_coding | tolerated_low_confidence(0.2) | benign(0) | TCGA-PG-A6IB-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VAMP2 | insertion | Nonsense_Mutation | novel | c.3_4insAAACTCTGTCTCTACTAAAAAAATACAAAATTAGCCGGGT | p.Asp2LysfsTer6 | p.D2Kfs*6 | protein_coding | TCGA-AX-A3FS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
VAMP2 | insertion | Frame_Shift_Ins | rs774244975 | c.35_36insC | p.Ala13CysfsTer19 | p.A13Cfs*19 | protein_coding | TCGA-DF-A2KN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD | |||
VAMP2 | insertion | Frame_Shift_Ins | rs774244975 | c.35_36insC | p.Ala13CysfsTer19 | p.A13Cfs*19 | protein_coding | TCGA-VQ-A91K-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | CR |
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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 |
6844 | VAMP2 | DRUGGABLE GENOME | BOTULINUM TOXIN TYPE B | |||
6844 | VAMP2 | DRUGGABLE GENOME | PMA | 17196367 | ||
6844 | VAMP2 | DRUGGABLE GENOME | INSULIN | INSULIN | 7796801,9267469,9430681,8973549 | |
6844 | VAMP2 | DRUGGABLE GENOME | inhibitor | CHEMBL1201569 | BOTULINUM TOXIN TYPE B | |
6844 | VAMP2 | DRUGGABLE GENOME | BOTULINUM TOXIN TYPE B |
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