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Gene: VSNL1 |
Gene summary for VSNL1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VSNL1 | Gene ID | 7447 |
| Gene name | visinin like 1 | |
| Gene Alias | HLP3 | |
| Cytomap | 2p24.2 | |
| Gene Type | protein-coding | GO ID | GO:0001678 | UniProtAcc | P62760 |
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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 |
| 7447 | VSNL1 | CA_HPV_1 | Human | Cervix | CC | 3.83e-04 | -1.30e-01 | 0.0264 |
| 7447 | VSNL1 | CA_HPV_3 | Human | Cervix | CC | 3.90e-22 | 4.60e-01 | 0.0414 |
| 7447 | VSNL1 | CCI_1 | Human | Cervix | CC | 4.90e-04 | 7.02e-01 | 0.528 |
| 7447 | VSNL1 | CCI_2 | Human | Cervix | CC | 1.95e-12 | 1.35e+00 | 0.5249 |
| 7447 | VSNL1 | CCI_3 | Human | Cervix | CC | 5.12e-06 | 7.47e-01 | 0.516 |
| 7447 | VSNL1 | Tumor | Human | Cervix | CC | 3.88e-29 | 5.96e-01 | 0.1241 |
| 7447 | VSNL1 | sample3 | Human | Cervix | CC | 3.78e-22 | 4.91e-01 | 0.1387 |
| 7447 | VSNL1 | H2 | Human | Cervix | HSIL_HPV | 4.00e-05 | -1.41e-01 | 0.0632 |
| 7447 | VSNL1 | T3 | Human | Cervix | CC | 3.83e-26 | 5.46e-01 | 0.1389 |
| 7447 | VSNL1 | LZE2T | Human | Esophagus | ESCC | 9.97e-05 | 9.94e-01 | 0.082 |
| 7447 | VSNL1 | LZE4T | Human | Esophagus | ESCC | 6.30e-09 | 3.78e-01 | 0.0811 |
| 7447 | VSNL1 | LZE7T | Human | Esophagus | ESCC | 5.27e-08 | 7.12e-01 | 0.0667 |
| 7447 | VSNL1 | LZE8T | Human | Esophagus | ESCC | 1.94e-08 | 8.66e-02 | 0.067 |
| 7447 | VSNL1 | P2T-E | Human | Esophagus | ESCC | 2.01e-24 | 8.33e-01 | 0.1177 |
| 7447 | VSNL1 | P4T-E | Human | Esophagus | ESCC | 7.66e-52 | 1.32e+00 | 0.1323 |
| 7447 | VSNL1 | P5T-E | Human | Esophagus | ESCC | 1.47e-32 | 9.51e-01 | 0.1327 |
| 7447 | VSNL1 | P9T-E | Human | Esophagus | ESCC | 7.52e-23 | 6.91e-01 | 0.1131 |
| 7447 | VSNL1 | P10T-E | Human | Esophagus | ESCC | 9.86e-62 | 1.29e+00 | 0.116 |
| 7447 | VSNL1 | P11T-E | Human | Esophagus | ESCC | 1.14e-13 | 9.87e-01 | 0.1426 |
| 7447 | VSNL1 | P12T-E | Human | Esophagus | ESCC | 2.53e-10 | 5.52e-01 | 0.1122 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:00512243 | Oral cavity | OSCC | negative regulation of protein transport | 70/7305 | 127/18723 | 1.65e-04 | 1.14e-03 | 70 |
| GO:003428420 | Oral cavity | OSCC | response to monosaccharide | 114/7305 | 225/18723 | 2.37e-04 | 1.54e-03 | 114 |
| GO:007133316 | Oral cavity | OSCC | cellular response to glucose stimulus | 79/7305 | 151/18723 | 5.97e-04 | 3.39e-03 | 79 |
| GO:000974619 | Oral cavity | OSCC | response to hexose | 109/7305 | 219/18723 | 7.41e-04 | 4.05e-03 | 109 |
| GO:000167816 | Oral cavity | OSCC | cellular glucose homeostasis | 88/7305 | 172/18723 | 7.74e-04 | 4.22e-03 | 88 |
| GO:007133116 | Oral cavity | OSCC | cellular response to hexose stimulus | 79/7305 | 153/18723 | 9.92e-04 | 5.17e-03 | 79 |
| GO:000930610 | Oral cavity | OSCC | protein secretion | 169/7305 | 359/18723 | 1.04e-03 | 5.34e-03 | 169 |
| GO:000974917 | Oral cavity | OSCC | response to glucose | 105/7305 | 212/18723 | 1.13e-03 | 5.78e-03 | 105 |
| GO:004259316 | Oral cavity | OSCC | glucose homeostasis | 125/7305 | 258/18723 | 1.21e-03 | 6.08e-03 | 125 |
| GO:003559210 | Oral cavity | OSCC | establishment of protein localization to extracellular region | 169/7305 | 360/18723 | 1.21e-03 | 6.08e-03 | 169 |
| GO:007132616 | Oral cavity | OSCC | cellular response to monosaccharide stimulus | 79/7305 | 154/18723 | 1.27e-03 | 6.33e-03 | 79 |
| GO:00716929 | Oral cavity | OSCC | protein localization to extracellular region | 172/7305 | 368/18723 | 1.40e-03 | 6.79e-03 | 172 |
| GO:003350016 | Oral cavity | OSCC | carbohydrate homeostasis | 125/7305 | 259/18723 | 1.44e-03 | 6.97e-03 | 125 |
| GO:00611788 | Oral cavity | OSCC | regulation of insulin secretion involved in cellular response to glucose stimulus | 37/7305 | 64/18723 | 1.76e-03 | 8.31e-03 | 37 |
| GO:007132217 | Oral cavity | OSCC | cellular response to carbohydrate stimulus | 82/7305 | 163/18723 | 2.14e-03 | 9.81e-03 | 82 |
| GO:005071414 | Oral cavity | OSCC | positive regulation of protein secretion | 70/7305 | 137/18723 | 2.64e-03 | 1.16e-02 | 70 |
| GO:00507089 | Oral cavity | OSCC | regulation of protein secretion | 126/7305 | 268/18723 | 4.41e-03 | 1.79e-02 | 126 |
| GO:00357736 | Oral cavity | OSCC | insulin secretion involved in cellular response to glucose stimulus | 40/7305 | 73/18723 | 4.45e-03 | 1.79e-02 | 40 |
| GO:00466761 | Oral cavity | OSCC | negative regulation of insulin secretion | 22/7305 | 38/18723 | 1.41e-02 | 4.66e-02 | 22 |
| GO:00357744 | Oral cavity | OSCC | positive regulation of insulin secretion involved in cellular response to glucose stimulus | 21/7305 | 36/18723 | 1.46e-02 | 4.76e-02 | 21 |
| Page: 1 2 3 4 5 6 |
| 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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| VSNL1 | SNV | Missense_Mutation | novel | c.355N>A | p.Val119Met | p.V119M | P62760 | protein_coding | deleterious(0.04) | benign(0.01) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VSNL1 | SNV | Missense_Mutation | c.103N>A | p.Leu35Ile | p.L35I | P62760 | protein_coding | tolerated(0.24) | benign(0.033) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| VSNL1 | SNV | Missense_Mutation | c.550N>A | p.Leu184Ile | p.L184I | P62760 | protein_coding | tolerated(0.42) | benign(0.38) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| VSNL1 | SNV | Missense_Mutation | novel | c.254N>C | p.Phe85Ser | p.F85S | P62760 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
| VSNL1 | SNV | Missense_Mutation | novel | c.29C>A | p.Pro10His | p.P10H | P62760 | protein_coding | deleterious(0.01) | probably_damaging(0.988) | TCGA-EO-A22X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unspecific | Carboplatin | Complete Response |
| VSNL1 | SNV | Missense_Mutation | novel | c.72N>C | p.Glu24Asp | p.E24D | P62760 | protein_coding | tolerated(0.31) | benign(0.007) | TCGA-EY-A1GP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| VSNL1 | SNV | Missense_Mutation | c.531N>A | p.Ser177Arg | p.S177R | P62760 | protein_coding | tolerated(0.48) | benign(0.019) | TCGA-44-2656-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| VSNL1 | SNV | Missense_Mutation | novel | c.490N>A | p.Asp164Asn | p.D164N | P62760 | protein_coding | tolerated(0.07) | benign(0.034) | TCGA-64-5781-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| VSNL1 | SNV | Missense_Mutation | novel | c.448N>G | p.Arg150Gly | p.R150G | P62760 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-78-7161-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| VSNL1 | SNV | Missense_Mutation | novel | c.500N>A | p.Thr167Lys | p.T167K | P62760 | protein_coding | deleterious(0.03) | benign(0.116) | TCGA-86-8279-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | etoposide | 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 |
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