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Gene: VAPA |
Gene summary for VAPA |
Gene summary. |
Gene information | Species | Human | Gene symbol | VAPA | Gene ID | 9218 |
Gene name | VAMP associated protein A | |
Gene Alias | VAMP-A | |
Cytomap | 18p11.22 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9P0L0 |
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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 |
9218 | VAPA | GSM4909285 | Human | Breast | IDC | 1.17e-03 | -1.03e-01 | 0.21 |
9218 | VAPA | GSM4909286 | Human | Breast | IDC | 5.23e-11 | -3.16e-01 | 0.1081 |
9218 | VAPA | GSM4909293 | Human | Breast | IDC | 2.76e-06 | -1.01e-01 | 0.1581 |
9218 | VAPA | GSM4909294 | Human | Breast | IDC | 2.65e-03 | -3.47e-01 | 0.2022 |
9218 | VAPA | GSM4909296 | Human | Breast | IDC | 4.32e-18 | -5.85e-01 | 0.1524 |
9218 | VAPA | GSM4909297 | Human | Breast | IDC | 4.20e-18 | -2.31e-01 | 0.1517 |
9218 | VAPA | GSM4909298 | Human | Breast | IDC | 2.58e-04 | -2.17e-01 | 0.1551 |
9218 | VAPA | GSM4909301 | Human | Breast | IDC | 2.56e-03 | -3.48e-01 | 0.1577 |
9218 | VAPA | GSM4909311 | Human | Breast | IDC | 1.84e-43 | -7.11e-01 | 0.1534 |
9218 | VAPA | GSM4909312 | Human | Breast | IDC | 3.79e-17 | -5.10e-01 | 0.1552 |
9218 | VAPA | GSM4909313 | Human | Breast | IDC | 3.54e-02 | -1.73e-01 | 0.0391 |
9218 | VAPA | GSM4909319 | Human | Breast | IDC | 5.22e-57 | -6.49e-01 | 0.1563 |
9218 | VAPA | GSM4909320 | Human | Breast | IDC | 1.70e-09 | -5.64e-01 | 0.1575 |
9218 | VAPA | GSM4909321 | Human | Breast | IDC | 4.62e-22 | -3.83e-01 | 0.1559 |
9218 | VAPA | brca1 | Human | Breast | Precancer | 4.59e-13 | 3.33e-01 | -0.0338 |
9218 | VAPA | brca2 | Human | Breast | Precancer | 1.17e-11 | 2.82e-01 | -0.024 |
9218 | VAPA | brca3 | Human | Breast | Precancer | 4.09e-12 | 3.45e-01 | -0.0263 |
9218 | VAPA | M1 | Human | Breast | IDC | 1.95e-05 | -4.29e-01 | 0.1577 |
9218 | VAPA | NCCBC14 | Human | Breast | DCIS | 2.88e-20 | -2.48e-01 | 0.2021 |
9218 | VAPA | NCCBC2 | Human | Breast | DCIS | 1.50e-05 | -2.53e-01 | 0.1554 |
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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:001907917 | Endometrium | EEC | viral genome replication | 42/2168 | 131/18723 | 3.43e-10 | 3.61e-08 | 42 |
GO:005170117 | Endometrium | EEC | biological process involved in interaction with host | 54/2168 | 203/18723 | 2.67e-09 | 2.01e-07 | 54 |
GO:005212617 | Endometrium | EEC | movement in host environment | 47/2168 | 175/18723 | 2.03e-08 | 1.23e-06 | 47 |
GO:007097215 | Endometrium | EEC | protein localization to endoplasmic reticulum | 24/2168 | 74/18723 | 1.59e-06 | 4.96e-05 | 24 |
GO:000690016 | Endometrium | EEC | vesicle budding from membrane | 21/2168 | 61/18723 | 2.40e-06 | 6.98e-05 | 21 |
GO:005079217 | Endometrium | EEC | regulation of viral process | 40/2168 | 164/18723 | 3.24e-06 | 8.85e-05 | 40 |
GO:004312216 | Endometrium | EEC | regulation of I-kappaB kinase/NF-kappaB signaling | 53/2168 | 249/18723 | 7.59e-06 | 1.73e-04 | 53 |
GO:004819313 | Endometrium | EEC | Golgi vesicle transport | 60/2168 | 296/18723 | 9.91e-06 | 2.17e-04 | 60 |
GO:190390017 | Endometrium | EEC | regulation of viral life cycle | 36/2168 | 148/18723 | 1.05e-05 | 2.25e-04 | 36 |
GO:004312314 | Endometrium | EEC | positive regulation of I-kappaB kinase/NF-kappaB signaling | 42/2168 | 186/18723 | 1.47e-05 | 2.87e-04 | 42 |
GO:000724915 | Endometrium | EEC | I-kappaB kinase/NF-kappaB signaling | 57/2168 | 281/18723 | 1.60e-05 | 3.12e-04 | 57 |
GO:004479412 | Endometrium | EEC | positive regulation by host of viral process | 7/2168 | 13/18723 | 2.51e-04 | 2.92e-03 | 7 |
GO:004478812 | Endometrium | EEC | modulation by host of viral process | 11/2168 | 30/18723 | 3.27e-04 | 3.61e-03 | 11 |
GO:000688812 | Endometrium | EEC | endoplasmic reticulum to Golgi vesicle-mediated transport | 29/2168 | 130/18723 | 3.63e-04 | 3.95e-03 | 29 |
GO:004390316 | Endometrium | EEC | regulation of biological process involved in symbiotic interaction | 19/2168 | 72/18723 | 4.11e-04 | 4.35e-03 | 19 |
GO:005181711 | Endometrium | EEC | modulation of process of other organism involved in symbiotic interaction | 20/2168 | 81/18723 | 7.45e-04 | 7.02e-03 | 20 |
GO:004852414 | Endometrium | EEC | positive regulation of viral process | 17/2168 | 65/18723 | 9.07e-04 | 8.22e-03 | 17 |
GO:005185112 | Endometrium | EEC | modulation by host of symbiont process | 15/2168 | 60/18723 | 2.88e-03 | 2.03e-02 | 15 |
GO:004482711 | Endometrium | EEC | modulation by host of viral genome replication | 7/2168 | 19/18723 | 3.94e-03 | 2.61e-02 | 7 |
GO:190390214 | Endometrium | EEC | positive regulation of viral life cycle | 9/2168 | 29/18723 | 4.24e-03 | 2.75e-02 | 9 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa049792 | Liver | Cirrhotic | Cholesterol metabolism | 30/2530 | 51/8465 | 1.59e-05 | 1.39e-04 | 8.60e-05 | 30 |
hsa049793 | Liver | Cirrhotic | Cholesterol metabolism | 30/2530 | 51/8465 | 1.59e-05 | 1.39e-04 | 8.60e-05 | 30 |
hsa049794 | Liver | HCC | Cholesterol metabolism | 41/4020 | 51/8465 | 1.33e-06 | 1.35e-05 | 7.49e-06 | 41 |
hsa049795 | Liver | HCC | Cholesterol metabolism | 41/4020 | 51/8465 | 1.33e-06 | 1.35e-05 | 7.49e-06 | 41 |
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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 |
VAPA | SNV | Missense_Mutation | rs376344309 | c.782N>T | p.Ser261Leu | p.S261L | Q9P0L0 | protein_coding | tolerated(0.22) | benign(0.306) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VAPA | SNV | Missense_Mutation | c.757C>G | p.His253Asp | p.H253D | Q9P0L0 | protein_coding | tolerated(0.41) | possibly_damaging(0.6) | TCGA-GM-A2DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | CR | |
VAPA | SNV | Missense_Mutation | rs773854854 | c.743T>C | p.Leu248Pro | p.L248P | Q9P0L0 | protein_coding | deleterious(0.02) | probably_damaging(0.988) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD |
VAPA | SNV | Missense_Mutation | c.128N>T | p.Ser43Leu | p.S43L | Q9P0L0 | protein_coding | deleterious(0.04) | probably_damaging(0.968) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
VAPA | SNV | Missense_Mutation | novel | c.194N>A | p.Ser65Asn | p.S65N | Q9P0L0 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VAPA | deletion | Frame_Shift_Del | c.348delN | p.Lys117AsnfsTer5 | p.K117Nfs*5 | Q9P0L0 | protein_coding | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
VAPA | SNV | Missense_Mutation | c.763N>A | p.Asp255Asn | p.D255N | Q9P0L0 | protein_coding | tolerated(0.29) | possibly_damaging(0.526) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
VAPA | SNV | Missense_Mutation | novel | c.248T>C | p.Phe83Ser | p.F83S | Q9P0L0 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AJ-A2QO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VAPA | SNV | Missense_Mutation | novel | c.461G>A | p.Ser154Asn | p.S154N | Q9P0L0 | protein_coding | tolerated(0.44) | benign(0.003) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VAPA | SNV | Missense_Mutation | rs773084616 | c.560N>C | p.Met187Thr | p.M187T | Q9P0L0 | protein_coding | deleterious(0.04) | benign(0.046) | TCGA-B5-A0JT-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Hormone Therapy | megace | SD |
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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 |
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