|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: VIRMA |
Gene summary for VIRMA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VIRMA | Gene ID | 25962 |
| Gene name | vir like m6A methyltransferase associated | |
| Gene Alias | KIAA1429 | |
| Cytomap | 8q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0001510 | UniProtAcc | Q69YN4 |
Top |
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 |
| 25962 | VIRMA | S014 | Human | Liver | HCC | 2.01e-41 | 1.26e+00 | 0.2254 |
| 25962 | VIRMA | S015 | Human | Liver | HCC | 4.22e-26 | 1.22e+00 | 0.2375 |
| 25962 | VIRMA | S016 | Human | Liver | HCC | 2.89e-39 | 1.29e+00 | 0.2243 |
| 25962 | VIRMA | S027 | Human | Liver | HCC | 1.27e-18 | 1.01e+00 | 0.2446 |
| 25962 | VIRMA | S028 | Human | Liver | HCC | 7.70e-30 | 1.05e+00 | 0.2503 |
| 25962 | VIRMA | S029 | Human | Liver | HCC | 1.11e-26 | 1.15e+00 | 0.2581 |
| 25962 | VIRMA | male-WTA | Human | Thyroid | PTC | 6.38e-17 | 2.30e-01 | 0.1037 |
| 25962 | VIRMA | PTC01 | Human | Thyroid | PTC | 2.77e-07 | 1.62e-01 | 0.1899 |
| 25962 | VIRMA | PTC03 | Human | Thyroid | PTC | 2.61e-05 | 2.29e-01 | 0.1784 |
| 25962 | VIRMA | PTC04 | Human | Thyroid | PTC | 5.71e-10 | 2.31e-01 | 0.1927 |
| 25962 | VIRMA | PTC05 | Human | Thyroid | PTC | 1.26e-11 | 3.79e-01 | 0.2065 |
| 25962 | VIRMA | PTC06 | Human | Thyroid | PTC | 5.27e-24 | 5.11e-01 | 0.2057 |
| 25962 | VIRMA | PTC07 | Human | Thyroid | PTC | 2.11e-25 | 3.80e-01 | 0.2044 |
| 25962 | VIRMA | ATC09 | Human | Thyroid | ATC | 2.66e-04 | 2.16e-01 | 0.2871 |
| 25962 | VIRMA | ATC12 | Human | Thyroid | ATC | 1.02e-18 | 3.96e-01 | 0.34 |
| 25962 | VIRMA | ATC13 | Human | Thyroid | ATC | 7.68e-49 | 8.56e-01 | 0.34 |
| 25962 | VIRMA | ATC1 | Human | Thyroid | ATC | 2.78e-04 | 2.20e-01 | 0.2878 |
| 25962 | VIRMA | ATC2 | Human | Thyroid | ATC | 1.80e-12 | 9.28e-01 | 0.34 |
| 25962 | VIRMA | ATC3 | Human | Thyroid | ATC | 6.43e-04 | 2.95e-01 | 0.338 |
| 25962 | VIRMA | ATC4 | Human | Thyroid | ATC | 2.41e-26 | 4.97e-01 | 0.34 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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. |
Top |
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:00314406 | Thyroid | PTC | regulation of mRNA 3'-end processing | 21/5968 | 28/18723 | 3.46e-06 | 4.46e-05 | 21 |
| GO:00436315 | Thyroid | PTC | RNA polyadenylation | 29/5968 | 45/18723 | 7.13e-06 | 8.38e-05 | 29 |
| GO:00063785 | Thyroid | PTC | mRNA polyadenylation | 28/5968 | 44/18723 | 1.46e-05 | 1.56e-04 | 28 |
| GO:00322594 | Thyroid | PTC | methylation | 146/5968 | 364/18723 | 4.99e-04 | 3.26e-03 | 146 |
| GO:00434145 | Thyroid | PTC | macromolecule methylation | 127/5968 | 316/18723 | 1.02e-03 | 6.07e-03 | 127 |
| GO:000838034 | Thyroid | ATC | RNA splicing | 270/6293 | 434/18723 | 7.50e-35 | 1.19e-31 | 270 |
| GO:190331134 | Thyroid | ATC | regulation of mRNA metabolic process | 181/6293 | 288/18723 | 1.75e-24 | 5.54e-22 | 181 |
| GO:005068434 | Thyroid | ATC | regulation of mRNA processing | 97/6293 | 137/18723 | 5.28e-19 | 7.25e-17 | 97 |
| GO:003112312 | Thyroid | ATC | RNA 3'-end processing | 65/6293 | 116/18723 | 5.58e-07 | 7.93e-06 | 65 |
| GO:003112413 | Thyroid | ATC | mRNA 3'-end processing | 40/6293 | 62/18723 | 6.25e-07 | 8.65e-06 | 40 |
| GO:003144014 | Thyroid | ATC | regulation of mRNA 3'-end processing | 21/6293 | 28/18723 | 8.94e-06 | 8.95e-05 | 21 |
| GO:004363112 | Thyroid | ATC | RNA polyadenylation | 29/6293 | 45/18723 | 2.26e-05 | 2.00e-04 | 29 |
| GO:000637812 | Thyroid | ATC | mRNA polyadenylation | 28/6293 | 44/18723 | 4.39e-05 | 3.54e-04 | 28 |
| GO:004341412 | Thyroid | ATC | macromolecule methylation | 131/6293 | 316/18723 | 2.01e-03 | 9.60e-03 | 131 |
| GO:003225911 | Thyroid | ATC | methylation | 148/6293 | 364/18723 | 2.69e-03 | 1.23e-02 | 148 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| Page: 1 |
Top |
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 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |