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Gene: VDAC2 |
Gene summary for VDAC2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | VDAC2 | Gene ID | 7417 |
Gene name | voltage dependent anion channel 2 | |
Gene Alias | POR | |
Cytomap | 10q22.2 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P45880 |
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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 |
7417 | VDAC2 | L1 | Human | Cervix | CC | 3.63e-06 | -5.71e-02 | 0.0802 |
7417 | VDAC2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.11e-19 | 1.03e+00 | -0.1808 |
7417 | VDAC2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.28e-12 | 7.73e-01 | -0.0811 |
7417 | VDAC2 | HTA11_78_2000001011 | Human | Colorectum | AD | 9.49e-21 | 7.85e-01 | -0.1088 |
7417 | VDAC2 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.26e-47 | 1.15e+00 | -0.1954 |
7417 | VDAC2 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.99e-08 | 1.35e+00 | -0.2602 |
7417 | VDAC2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.12e-08 | 9.91e-01 | -0.2196 |
7417 | VDAC2 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.80e-02 | 4.03e-01 | -0.1526 |
7417 | VDAC2 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.01e-04 | 3.68e-01 | -0.1464 |
7417 | VDAC2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.13e-14 | 7.47e-01 | -0.059 |
7417 | VDAC2 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.25e-09 | 9.11e-01 | -0.1706 |
7417 | VDAC2 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.78e-10 | 8.94e-01 | -0.2061 |
7417 | VDAC2 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.67e-03 | 2.47e-01 | 0.096 |
7417 | VDAC2 | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.11e-02 | 5.04e-01 | 0.0446 |
7417 | VDAC2 | HTA11_6801_2000001011 | Human | Colorectum | SER | 6.35e-08 | 9.05e-01 | 0.0171 |
7417 | VDAC2 | HTA11_7469_2000001011 | Human | Colorectum | AD | 9.00e-05 | 6.93e-01 | -0.0124 |
7417 | VDAC2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 7.05e-10 | 5.37e-01 | 0.294 |
7417 | VDAC2 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 4.68e-10 | 1.38e+00 | 0.3487 |
7417 | VDAC2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.60e-05 | 4.74e-01 | 0.281 |
7417 | VDAC2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 9.85e-18 | 8.04e-01 | 0.3859 |
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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:00971939 | Breast | Precancer | intrinsic apoptotic signaling pathway | 59/1080 | 288/18723 | 8.07e-18 | 3.60e-15 | 59 |
GO:20012339 | Breast | Precancer | regulation of apoptotic signaling pathway | 65/1080 | 356/18723 | 7.70e-17 | 3.17e-14 | 65 |
GO:20012429 | Breast | Precancer | regulation of intrinsic apoptotic signaling pathway | 41/1080 | 164/18723 | 6.48e-16 | 2.31e-13 | 41 |
GO:00068398 | Breast | Precancer | mitochondrial transport | 45/1080 | 254/18723 | 1.37e-11 | 1.88e-09 | 45 |
GO:20012349 | Breast | Precancer | negative regulation of apoptotic signaling pathway | 39/1080 | 224/18723 | 5.35e-10 | 4.77e-08 | 39 |
GO:20012439 | Breast | Precancer | negative regulation of intrinsic apoptotic signaling pathway | 23/1080 | 98/18723 | 5.82e-09 | 4.45e-07 | 23 |
GO:00086378 | Breast | Precancer | apoptotic mitochondrial changes | 23/1080 | 107/18723 | 3.44e-08 | 2.12e-06 | 23 |
GO:00432549 | Breast | Precancer | regulation of protein-containing complex assembly | 50/1080 | 428/18723 | 1.63e-06 | 5.97e-05 | 50 |
GO:00070066 | Breast | Precancer | mitochondrial membrane organization | 20/1080 | 116/18723 | 9.88e-06 | 2.61e-04 | 20 |
GO:00905595 | Breast | Precancer | regulation of membrane permeability | 15/1080 | 78/18723 | 3.35e-05 | 7.29e-04 | 15 |
GO:00469025 | Breast | Precancer | regulation of mitochondrial membrane permeability | 13/1080 | 63/18723 | 5.13e-05 | 1.07e-03 | 13 |
GO:0035036 | Breast | Precancer | sperm-egg recognition | 10/1080 | 48/18723 | 3.43e-04 | 4.81e-03 | 10 |
GO:00973456 | Breast | Precancer | mitochondrial outer membrane permeabilization | 8/1080 | 32/18723 | 3.62e-04 | 5.00e-03 | 8 |
GO:0007339 | Breast | Precancer | binding of sperm to zona pellucida | 9/1080 | 40/18723 | 3.69e-04 | 5.03e-03 | 9 |
GO:0009988 | Breast | Precancer | cell-cell recognition | 12/1080 | 68/18723 | 4.63e-04 | 6.12e-03 | 12 |
GO:00357945 | Breast | Precancer | positive regulation of mitochondrial membrane permeability | 9/1080 | 43/18723 | 6.51e-04 | 7.99e-03 | 9 |
GO:19021084 | Breast | Precancer | regulation of mitochondrial membrane permeability involved in apoptotic process | 9/1080 | 45/18723 | 9.22e-04 | 1.05e-02 | 9 |
GO:19021105 | Breast | Precancer | positive regulation of mitochondrial membrane permeability involved in apoptotic process | 8/1080 | 38/18723 | 1.24e-03 | 1.32e-02 | 8 |
GO:00313338 | Breast | Precancer | negative regulation of protein-containing complex assembly | 18/1080 | 141/18723 | 1.27e-03 | 1.35e-02 | 18 |
GO:19057105 | Breast | Precancer | positive regulation of membrane permeability | 9/1080 | 48/18723 | 1.49e-03 | 1.54e-02 | 9 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501218 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
hsa0502016 | Breast | Precancer | Prion disease | 95/684 | 273/8465 | 1.39e-37 | 1.46e-35 | 1.12e-35 | 95 |
hsa0501616 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
hsa0501016 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
hsa0502216 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
hsa0520818 | Breast | Precancer | Chemical carcinogenesis - reactive oxygen species | 68/684 | 223/8465 | 3.61e-23 | 1.14e-21 | 8.73e-22 | 68 |
hsa0541518 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
hsa0501714 | Breast | Precancer | Spinocerebellar ataxia | 29/684 | 143/8465 | 2.79e-06 | 3.83e-05 | 2.94e-05 | 29 |
hsa042189 | Breast | Precancer | Cellular senescence | 29/684 | 156/8465 | 1.66e-05 | 1.69e-04 | 1.30e-04 | 29 |
hsa0421610 | Breast | Precancer | Ferroptosis | 11/684 | 41/8465 | 2.95e-04 | 2.45e-03 | 1.88e-03 | 11 |
hsa0516618 | Breast | Precancer | Human T-cell leukemia virus 1 infection | 33/684 | 222/8465 | 4.29e-04 | 3.31e-03 | 2.53e-03 | 33 |
hsa0501219 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
hsa0502017 | Breast | Precancer | Prion disease | 95/684 | 273/8465 | 1.39e-37 | 1.46e-35 | 1.12e-35 | 95 |
hsa0501617 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
hsa0501017 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
hsa0502217 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
hsa0520819 | Breast | Precancer | Chemical carcinogenesis - reactive oxygen species | 68/684 | 223/8465 | 3.61e-23 | 1.14e-21 | 8.73e-22 | 68 |
hsa0541519 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
hsa0501715 | Breast | Precancer | Spinocerebellar ataxia | 29/684 | 143/8465 | 2.79e-06 | 3.83e-05 | 2.94e-05 | 29 |
hsa0421814 | Breast | Precancer | Cellular senescence | 29/684 | 156/8465 | 1.66e-05 | 1.69e-04 | 1.30e-04 | 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 |
VDAC2 | SNV | Missense_Mutation | novel | c.731N>A | p.Arg244His | p.R244H | P45880 | protein_coding | tolerated(0.13) | benign(0.007) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VDAC2 | SNV | Missense_Mutation | c.698N>T | p.Asn233Ile | p.N233I | P45880 | protein_coding | deleterious(0.01) | possibly_damaging(0.582) | TCGA-AN-A0FD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VDAC2 | SNV | Missense_Mutation | novel | c.862C>G | p.Leu288Val | p.L288V | P45880 | protein_coding | tolerated(0.06) | benign(0.027) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VDAC2 | SNV | Missense_Mutation | novel | c.311A>C | p.Asp104Ala | p.D104A | P45880 | protein_coding | deleterious(0) | benign(0.14) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
VDAC2 | SNV | Missense_Mutation | rs759303647 | c.910G>A | p.Ala304Thr | p.A304T | P45880 | protein_coding | deleterious(0.02) | benign(0.221) | TCGA-D5-6930-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
VDAC2 | SNV | Missense_Mutation | c.223N>G | p.Thr75Ala | p.T75A | P45880 | protein_coding | tolerated(0.09) | benign(0.003) | TCGA-RU-A8FL-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD | |
VDAC2 | SNV | Missense_Mutation | rs759303647 | c.910G>A | p.Ala304Thr | p.A304T | P45880 | protein_coding | deleterious(0.02) | benign(0.221) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VDAC2 | deletion | Frame_Shift_Del | c.177_178delNN | p.Lys60ValfsTer14 | p.K60Vfs*14 | P45880 | protein_coding | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |||
VDAC2 | SNV | Missense_Mutation | novel | c.83N>A | p.Cys28Tyr | p.C28Y | P45880 | protein_coding | deleterious(0) | benign(0.245) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
VDAC2 | SNV | Missense_Mutation | novel | c.157G>T | p.Val53Leu | p.V53L | P45880 | protein_coding | tolerated(0.16) | benign(0.01) | TCGA-AJ-A23O-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | 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 |
7417 | VDAC2 | NA | OLESOXIME | OLESOXIME | ||
7417 | VDAC2 | NA | TCDD | 17998243 |
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