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Gene: VANGL2 |
Gene summary for VANGL2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VANGL2 | Gene ID | 57216 |
| Gene name | VANGL planar cell polarity protein 2 | |
| Gene Alias | LPP1 | |
| Cytomap | 1q23.2 | |
| Gene Type | protein-coding | GO ID | GO:0001655 | UniProtAcc | A8K4L6 |
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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 |
| 57216 | VANGL2 | LZE2T | Human | Esophagus | ESCC | 2.72e-02 | 2.73e-01 | 0.082 |
| 57216 | VANGL2 | LZE7T | Human | Esophagus | ESCC | 1.46e-08 | 3.15e-01 | 0.0667 |
| 57216 | VANGL2 | LZE24T | Human | Esophagus | ESCC | 1.19e-06 | 1.90e-01 | 0.0596 |
| 57216 | VANGL2 | P2T-E | Human | Esophagus | ESCC | 2.39e-14 | 3.05e-01 | 0.1177 |
| 57216 | VANGL2 | P4T-E | Human | Esophagus | ESCC | 1.20e-12 | 2.68e-01 | 0.1323 |
| 57216 | VANGL2 | P5T-E | Human | Esophagus | ESCC | 1.46e-10 | 9.78e-02 | 0.1327 |
| 57216 | VANGL2 | P8T-E | Human | Esophagus | ESCC | 8.86e-05 | 5.45e-02 | 0.0889 |
| 57216 | VANGL2 | P9T-E | Human | Esophagus | ESCC | 9.40e-05 | 1.13e-01 | 0.1131 |
| 57216 | VANGL2 | P10T-E | Human | Esophagus | ESCC | 2.30e-10 | 2.35e-01 | 0.116 |
| 57216 | VANGL2 | P12T-E | Human | Esophagus | ESCC | 2.14e-05 | 1.23e-01 | 0.1122 |
| 57216 | VANGL2 | P15T-E | Human | Esophagus | ESCC | 3.66e-08 | 2.06e-01 | 0.1149 |
| 57216 | VANGL2 | P20T-E | Human | Esophagus | ESCC | 4.22e-06 | 1.91e-01 | 0.1124 |
| 57216 | VANGL2 | P21T-E | Human | Esophagus | ESCC | 5.05e-12 | 2.25e-01 | 0.1617 |
| 57216 | VANGL2 | P22T-E | Human | Esophagus | ESCC | 3.85e-12 | 2.25e-01 | 0.1236 |
| 57216 | VANGL2 | P23T-E | Human | Esophagus | ESCC | 6.35e-05 | 1.50e-01 | 0.108 |
| 57216 | VANGL2 | P26T-E | Human | Esophagus | ESCC | 4.67e-10 | 2.33e-01 | 0.1276 |
| 57216 | VANGL2 | P27T-E | Human | Esophagus | ESCC | 2.84e-04 | 1.18e-01 | 0.1055 |
| 57216 | VANGL2 | P28T-E | Human | Esophagus | ESCC | 2.50e-15 | 2.67e-01 | 0.1149 |
| 57216 | VANGL2 | P30T-E | Human | Esophagus | ESCC | 3.46e-13 | 5.02e-01 | 0.137 |
| 57216 | VANGL2 | P31T-E | Human | Esophagus | ESCC | 2.01e-07 | 1.31e-01 | 0.1251 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:001605517 | Esophagus | ESCC | Wnt signaling pathway | 268/8552 | 444/18723 | 2.32e-10 | 6.58e-09 | 268 |
| GO:019873817 | Esophagus | ESCC | cell-cell signaling by wnt | 269/8552 | 446/18723 | 2.41e-10 | 6.79e-09 | 269 |
| GO:000184115 | Esophagus | ESCC | neural tube formation | 75/8552 | 102/18723 | 9.68e-09 | 1.95e-07 | 75 |
| GO:000184314 | Esophagus | ESCC | neural tube closure | 66/8552 | 88/18723 | 1.98e-08 | 3.82e-07 | 66 |
| GO:001402014 | Esophagus | ESCC | primary neural tube formation | 69/8552 | 94/18723 | 4.22e-08 | 7.76e-07 | 69 |
| GO:006060614 | Esophagus | ESCC | tube closure | 66/8552 | 89/18723 | 4.24e-08 | 7.76e-07 | 66 |
| GO:00219159 | Esophagus | ESCC | neural tube development | 101/8552 | 152/18723 | 1.78e-07 | 2.79e-06 | 101 |
| GO:00163316 | Esophagus | ESCC | morphogenesis of embryonic epithelium | 98/8552 | 147/18723 | 2.12e-07 | 3.27e-06 | 98 |
| GO:000183814 | Esophagus | ESCC | embryonic epithelial tube formation | 83/8552 | 121/18723 | 2.78e-07 | 4.08e-06 | 83 |
| GO:003514815 | Esophagus | ESCC | tube formation | 96/8552 | 148/18723 | 1.86e-06 | 2.16e-05 | 96 |
| GO:00721759 | Esophagus | ESCC | epithelial tube formation | 86/8552 | 132/18723 | 4.81e-06 | 5.10e-05 | 86 |
| GO:006056210 | Esophagus | ESCC | epithelial tube morphogenesis | 187/8552 | 325/18723 | 9.95e-06 | 9.44e-05 | 187 |
| GO:00017387 | Esophagus | ESCC | morphogenesis of a polarized epithelium | 63/8552 | 94/18723 | 2.34e-05 | 2.00e-04 | 63 |
| GO:00600714 | Esophagus | ESCC | Wnt signaling pathway, planar cell polarity pathway | 36/8552 | 52/18723 | 5.05e-04 | 2.79e-03 | 36 |
| GO:00485687 | Esophagus | ESCC | embryonic organ development | 228/8552 | 427/18723 | 7.28e-04 | 3.79e-03 | 228 |
| GO:00901753 | Esophagus | ESCC | regulation of establishment of planar polarity | 37/8552 | 56/18723 | 1.65e-03 | 7.65e-03 | 37 |
| GO:00017361 | Esophagus | ESCC | establishment of planar polarity | 45/8552 | 72/18723 | 2.97e-03 | 1.24e-02 | 45 |
| GO:00071641 | Esophagus | ESCC | establishment of tissue polarity | 45/8552 | 72/18723 | 2.97e-03 | 1.24e-02 | 45 |
| GO:00355671 | Esophagus | ESCC | non-canonical Wnt signaling pathway | 45/8552 | 72/18723 | 2.97e-03 | 1.24e-02 | 45 |
| GO:19055153 | Esophagus | ESCC | non-motile cilium assembly | 39/8552 | 61/18723 | 3.08e-03 | 1.28e-02 | 39 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| VANGL2 | SNV | Missense_Mutation | rs201184424 | c.457G>A | p.Ala153Thr | p.A153T | Q9ULK5 | protein_coding | tolerated(0.07) | probably_damaging(0.994) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VANGL2 | SNV | Missense_Mutation | rs372488057 | c.1429N>A | p.Val477Ile | p.V477I | Q9ULK5 | protein_coding | tolerated(0.18) | probably_damaging(0.984) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VANGL2 | SNV | Missense_Mutation | c.365N>T | p.Thr122Met | p.T122M | Q9ULK5 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AN-A0FW-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| VANGL2 | SNV | Missense_Mutation | c.1014N>G | p.His338Gln | p.H338Q | Q9ULK5 | protein_coding | deleterious(0.01) | probably_damaging(0.992) | TCGA-B6-A0RG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| VANGL2 | SNV | Missense_Mutation | c.505N>T | p.Arg169Cys | p.R169C | Q9ULK5 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-BH-A0RX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | SD | |
| VANGL2 | SNV | Missense_Mutation | rs536256783 | c.751G>A | p.Val251Met | p.V251M | Q9ULK5 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VANGL2 | SNV | Missense_Mutation | c.59N>T | p.Ser20Phe | p.S20F | Q9ULK5 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| VANGL2 | SNV | Missense_Mutation | c.227C>T | p.Thr76Met | p.T76M | Q9ULK5 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-E2-A158-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | arimidex | SD | |
| VANGL2 | SNV | Missense_Mutation | c.179G>A | p.Arg60Gln | p.R60Q | Q9ULK5 | protein_coding | tolerated(0.13) | possibly_damaging(0.854) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| VANGL2 | SNV | Missense_Mutation | novel | c.1055T>C | p.Val352Ala | p.V352A | Q9ULK5 | protein_coding | deleterious(0.03) | benign(0.187) | TCGA-C5-A2M1-01 | Cervix | cervical & endocervical cancer | 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 |
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