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Gene: VEGFA |
Gene summary for VEGFA |
Gene summary. |
Gene information | Species | Human | Gene symbol | VEGFA | Gene ID | 7422 |
Gene name | vascular endothelial growth factor A | |
Gene Alias | MVCD1 | |
Cytomap | 6p21.1 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A087WUD8 |
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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 |
7422 | VEGFA | GSM4909281 | Human | Breast | IDC | 5.30e-08 | 4.70e-01 | 0.21 |
7422 | VEGFA | GSM4909286 | Human | Breast | IDC | 4.66e-03 | -2.45e-01 | 0.1081 |
7422 | VEGFA | GSM4909294 | Human | Breast | IDC | 2.50e-02 | -2.41e-01 | 0.2022 |
7422 | VEGFA | GSM4909296 | Human | Breast | IDC | 1.34e-05 | -1.79e-01 | 0.1524 |
7422 | VEGFA | GSM4909297 | Human | Breast | IDC | 3.44e-09 | -2.82e-01 | 0.1517 |
7422 | VEGFA | GSM4909298 | Human | Breast | IDC | 1.98e-02 | -2.47e-01 | 0.1551 |
7422 | VEGFA | GSM4909311 | Human | Breast | IDC | 6.77e-14 | -2.78e-01 | 0.1534 |
7422 | VEGFA | GSM4909312 | Human | Breast | IDC | 5.10e-07 | -2.63e-01 | 0.1552 |
7422 | VEGFA | GSM4909313 | Human | Breast | IDC | 6.95e-05 | -2.88e-01 | 0.0391 |
7422 | VEGFA | GSM4909315 | Human | Breast | IDC | 1.34e-02 | 3.31e-01 | 0.21 |
7422 | VEGFA | GSM4909319 | Human | Breast | IDC | 1.44e-17 | -3.14e-01 | 0.1563 |
7422 | VEGFA | GSM4909320 | Human | Breast | IDC | 3.24e-02 | -6.03e-02 | 0.1575 |
7422 | VEGFA | GSM4909321 | Human | Breast | IDC | 3.53e-13 | -3.26e-01 | 0.1559 |
7422 | VEGFA | ctrl6 | Human | Breast | Precancer | 6.56e-15 | 7.40e-01 | -0.0061 |
7422 | VEGFA | brca1 | Human | Breast | Precancer | 2.78e-10 | -2.94e-01 | -0.0338 |
7422 | VEGFA | brca10 | Human | Breast | Precancer | 2.93e-33 | 8.67e-01 | -0.0029 |
7422 | VEGFA | NCCBC14 | Human | Breast | DCIS | 3.70e-04 | -9.47e-02 | 0.2021 |
7422 | VEGFA | NCCBC2 | Human | Breast | DCIS | 3.20e-02 | 2.72e-01 | 0.1554 |
7422 | VEGFA | NCCBC5 | Human | Breast | DCIS | 1.17e-03 | -5.01e-02 | 0.2046 |
7422 | VEGFA | P1 | Human | Breast | IDC | 2.33e-07 | -6.81e-02 | 0.1527 |
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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:00380665 | Endometrium | AEH | p38MAPK cascade | 18/2100 | 55/18723 | 1.77e-05 | 3.65e-04 | 18 |
GO:00015589 | Endometrium | AEH | regulation of cell growth | 75/2100 | 414/18723 | 1.79e-05 | 3.65e-04 | 75 |
GO:00435428 | Endometrium | AEH | endothelial cell migration | 55/2100 | 279/18723 | 2.11e-05 | 4.15e-04 | 55 |
GO:00105955 | Endometrium | AEH | positive regulation of endothelial cell migration | 32/2100 | 133/18723 | 2.12e-05 | 4.15e-04 | 32 |
GO:00611384 | Endometrium | AEH | morphogenesis of a branching epithelium | 40/2100 | 182/18723 | 2.16e-05 | 4.20e-04 | 40 |
GO:00434105 | Endometrium | AEH | positive regulation of MAPK cascade | 84/2100 | 480/18723 | 2.19e-05 | 4.25e-04 | 84 |
GO:00018224 | Endometrium | AEH | kidney development | 57/2100 | 293/18723 | 2.25e-05 | 4.35e-04 | 57 |
GO:00703028 | Endometrium | AEH | regulation of stress-activated protein kinase signaling cascade | 42/2100 | 195/18723 | 2.27e-05 | 4.35e-04 | 42 |
GO:00482598 | Endometrium | AEH | regulation of receptor-mediated endocytosis | 28/2100 | 110/18723 | 2.28e-05 | 4.35e-04 | 28 |
GO:00485887 | Endometrium | AEH | developmental cell growth | 48/2100 | 234/18723 | 2.39e-05 | 4.53e-04 | 48 |
GO:00017637 | Endometrium | AEH | morphogenesis of a branching structure | 42/2100 | 196/18723 | 2.58e-05 | 4.86e-04 | 42 |
GO:002240714 | Endometrium | AEH | regulation of cell-cell adhesion | 79/2100 | 448/18723 | 2.90e-05 | 5.40e-04 | 79 |
GO:19901386 | Endometrium | AEH | neuron projection extension | 38/2100 | 172/18723 | 3.03e-05 | 5.56e-04 | 38 |
GO:00301009 | Endometrium | AEH | regulation of endocytosis | 44/2100 | 211/18723 | 3.39e-05 | 6.05e-04 | 44 |
GO:00068988 | Endometrium | AEH | receptor-mediated endocytosis | 49/2100 | 244/18723 | 3.54e-05 | 6.24e-04 | 49 |
GO:00107207 | Endometrium | AEH | positive regulation of cell development | 57/2100 | 298/18723 | 3.72e-05 | 6.49e-04 | 57 |
GO:00019549 | Endometrium | AEH | positive regulation of cell-matrix adhesion | 18/2100 | 58/18723 | 3.98e-05 | 6.86e-04 | 18 |
GO:00105945 | Endometrium | AEH | regulation of endothelial cell migration | 47/2100 | 232/18723 | 4.02e-05 | 6.91e-04 | 47 |
GO:004887216 | Endometrium | AEH | homeostasis of number of cells | 53/2100 | 272/18723 | 4.10e-05 | 6.99e-04 | 53 |
GO:007048215 | Endometrium | AEH | response to oxygen levels | 64/2100 | 347/18723 | 4.11e-05 | 6.99e-04 | 64 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0520818 | Breast | Precancer | Chemical carcinogenesis - reactive oxygen species | 68/684 | 223/8465 | 3.61e-23 | 1.14e-21 | 8.73e-22 | 68 |
hsa0516718 | Breast | Precancer | Kaposi sarcoma-associated herpesvirus infection | 36/684 | 194/8465 | 1.68e-06 | 2.53e-05 | 1.94e-05 | 36 |
hsa0541818 | Breast | Precancer | Fluid shear stress and atherosclerosis | 28/684 | 139/8465 | 4.74e-06 | 6.00e-05 | 4.59e-05 | 28 |
hsa0406616 | Breast | Precancer | HIF-1 signaling pathway | 23/684 | 109/8465 | 1.51e-05 | 1.59e-04 | 1.22e-04 | 23 |
hsa0532312 | Breast | Precancer | Rheumatoid arthritis | 19/684 | 93/8465 | 1.30e-04 | 1.14e-03 | 8.73e-04 | 19 |
hsa0520514 | Breast | Precancer | Proteoglycans in cancer | 30/684 | 205/8465 | 1.00e-03 | 7.18e-03 | 5.50e-03 | 30 |
hsa0516316 | Breast | Precancer | Human cytomegalovirus infection | 32/684 | 225/8465 | 1.13e-03 | 7.57e-03 | 5.80e-03 | 32 |
hsa052196 | Breast | Precancer | Bladder cancer | 9/684 | 41/8465 | 4.65e-03 | 2.72e-02 | 2.08e-02 | 9 |
hsa0520819 | Breast | Precancer | Chemical carcinogenesis - reactive oxygen species | 68/684 | 223/8465 | 3.61e-23 | 1.14e-21 | 8.73e-22 | 68 |
hsa0516719 | Breast | Precancer | Kaposi sarcoma-associated herpesvirus infection | 36/684 | 194/8465 | 1.68e-06 | 2.53e-05 | 1.94e-05 | 36 |
hsa0541819 | Breast | Precancer | Fluid shear stress and atherosclerosis | 28/684 | 139/8465 | 4.74e-06 | 6.00e-05 | 4.59e-05 | 28 |
hsa0406617 | Breast | Precancer | HIF-1 signaling pathway | 23/684 | 109/8465 | 1.51e-05 | 1.59e-04 | 1.22e-04 | 23 |
hsa0532313 | Breast | Precancer | Rheumatoid arthritis | 19/684 | 93/8465 | 1.30e-04 | 1.14e-03 | 8.73e-04 | 19 |
hsa0520515 | Breast | Precancer | Proteoglycans in cancer | 30/684 | 205/8465 | 1.00e-03 | 7.18e-03 | 5.50e-03 | 30 |
hsa0516317 | Breast | Precancer | Human cytomegalovirus infection | 32/684 | 225/8465 | 1.13e-03 | 7.57e-03 | 5.80e-03 | 32 |
hsa0521913 | Breast | Precancer | Bladder cancer | 9/684 | 41/8465 | 4.65e-03 | 2.72e-02 | 2.08e-02 | 9 |
hsa0520824 | Breast | IDC | Chemical carcinogenesis - reactive oxygen species | 71/867 | 223/8465 | 2.55e-19 | 7.53e-18 | 5.63e-18 | 71 |
hsa0541824 | Breast | IDC | Fluid shear stress and atherosclerosis | 34/867 | 139/8465 | 9.41e-07 | 1.61e-05 | 1.20e-05 | 34 |
hsa0520523 | Breast | IDC | Proteoglycans in cancer | 42/867 | 205/8465 | 7.69e-06 | 9.99e-05 | 7.48e-05 | 42 |
hsa0516723 | Breast | IDC | Kaposi sarcoma-associated herpesvirus infection | 38/867 | 194/8465 | 5.87e-05 | 5.96e-04 | 4.46e-04 | 38 |
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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 |
VEGFA | FLT1 | VEGFA_VEGFR1 | VEGF | Breast | ADJ |
VEGFA | KDR | VEGFA_VEGFR2 | VEGF | Breast | ADJ |
VEGFA | FLT1_KDR | VEGFA_VEGFR1R2 | VEGF | Breast | ADJ |
VEGFA | FLT1 | VEGFA_VEGFR1 | VEGF | Breast | DCIS |
VEGFA | FLT1 | VEGFA_VEGFR1 | VEGF | Breast | Healthy |
VEGFA | KDR | VEGFA_VEGFR2 | VEGF | Breast | Healthy |
VEGFA | FLT1_KDR | VEGFA_VEGFR1R2 | VEGF | Breast | Healthy |
VEGFA | FLT1 | VEGFA_VEGFR1 | VEGF | Breast | IDC |
VEGFA | KDR | VEGFA_VEGFR2 | VEGF | Breast | IDC |
VEGFA | FLT1_KDR | VEGFA_VEGFR1R2 | VEGF | Breast | IDC |
VEGFA | FLT1 | VEGFA_VEGFR1 | VEGF | Breast | Precancer |
VEGFA | FLT1 | VEGFA_VEGFR1 | VEGF | Cervix | ADJ |
VEGFA | KDR | VEGFA_VEGFR2 | VEGF | Cervix | ADJ |
VEGFA | FLT1_KDR | VEGFA_VEGFR1R2 | VEGF | Cervix | ADJ |
VEGFA | FLT1 | VEGFA_VEGFR1 | VEGF | Cervix | CC |
VEGFA | KDR | VEGFA_VEGFR2 | VEGF | Cervix | CC |
VEGFA | FLT1_KDR | VEGFA_VEGFR1R2 | VEGF | Cervix | CC |
VEGFA | FLT1 | VEGFA_VEGFR1 | VEGF | Cervix | Healthy |
VEGFA | KDR | VEGFA_VEGFR2 | VEGF | Cervix | Healthy |
VEGFA | FLT1_KDR | VEGFA_VEGFR1R2 | VEGF | Cervix | Healthy |
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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 |
VEGFA | SNV | Missense_Mutation | novel | c.1235N>T | p.Arg412Leu | p.R412L | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A0ST-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
VEGFA | SNV | Missense_Mutation | novel | c.1102T>C | p.Ser368Pro | p.S368P | protein_coding | tolerated(0.06) | probably_damaging(0.991) | TCGA-B6-A0I6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
VEGFA | SNV | Missense_Mutation | rs753526479 | c.1073N>C | p.Leu358Pro | p.L358P | protein_coding | tolerated_low_confidence(0.38) | possibly_damaging(0.549) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
VEGFA | SNV | Missense_Mutation | c.742G>A | p.Glu248Lys | p.E248K | protein_coding | tolerated(0.07) | possibly_damaging(0.526) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
VEGFA | SNV | Missense_Mutation | rs376388064 | c.1136N>T | p.Pro379Leu | p.P379L | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
VEGFA | SNV | Missense_Mutation | c.1174N>T | p.Arg392Cys | p.R392C | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
VEGFA | SNV | Missense_Mutation | rs369593555 | c.1175G>A | p.Arg392His | p.R392H | protein_coding | tolerated(0.11) | possibly_damaging(0.761) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
VEGFA | SNV | Missense_Mutation | novel | c.538N>G | p.Thr180Ala | p.T180A | protein_coding | tolerated_low_confidence(0.06) | benign(0.342) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
VEGFA | SNV | Missense_Mutation | c.128N>T | p.Glu43Val | p.E43V | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.994) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | ||
VEGFA | insertion | Frame_Shift_Ins | novel | c.1158_1159insA | p.Asn388LysfsTer12 | p.N388Kfs*12 | protein_coding | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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 |
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | ANTHRACYCLINE | 15297400 | ||
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | Carbamide derivative 17 | |||
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | inhibitor | SORAFENIB TOSYLATE | ||
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | Carbamide derivative 21 | |||
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | FENOFIBRATE | FENOFIBRATE | 11356390 | |
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | Quinoline and quinazoline derivative 4 | |||
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | Navicixizumab | NAVICIXIZUMAB | ||
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | inhibitor | CHEMBL1742982 | AFLIBERCEPT | |
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | PENTOSAN POLYSULFATE | 17071199 | ||
7422 | VEGFA | CLINICALLY ACTIONABLE, GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME | Carbamide derivative 20 |
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