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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 |
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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 |
| 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. |
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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:000838022 | Liver | HCC | RNA splicing | 313/7958 | 434/18723 | 1.36e-36 | 1.73e-33 | 313 |
| GO:190331121 | Liver | HCC | regulation of mRNA metabolic process | 205/7958 | 288/18723 | 3.38e-23 | 6.90e-21 | 205 |
| GO:005068421 | Liver | HCC | regulation of mRNA processing | 106/7958 | 137/18723 | 7.64e-17 | 7.12e-15 | 106 |
| GO:00311241 | Liver | HCC | mRNA 3'-end processing | 50/7958 | 62/18723 | 8.44e-10 | 2.60e-08 | 50 |
| GO:00311231 | Liver | HCC | RNA 3'-end processing | 81/7958 | 116/18723 | 2.27e-09 | 6.32e-08 | 81 |
| GO:00434141 | Liver | HCC | macromolecule methylation | 183/7958 | 316/18723 | 2.00e-08 | 4.72e-07 | 183 |
| GO:00314401 | Liver | HCC | regulation of mRNA 3'-end processing | 26/7958 | 28/18723 | 2.82e-08 | 6.43e-07 | 26 |
| GO:0032259 | Liver | HCC | methylation | 206/7958 | 364/18723 | 3.35e-08 | 7.53e-07 | 206 |
| GO:0006378 | Liver | HCC | mRNA polyadenylation | 35/7958 | 44/18723 | 5.70e-07 | 9.03e-06 | 35 |
| GO:0043631 | Liver | HCC | RNA polyadenylation | 35/7958 | 45/18723 | 1.51e-06 | 2.15e-05 | 35 |
| GO:0009451 | Liver | HCC | RNA modification | 101/7958 | 167/18723 | 2.02e-06 | 2.78e-05 | 101 |
| GO:1900363 | Liver | HCC | regulation of mRNA polyadenylation | 16/7958 | 17/18723 | 1.15e-05 | 1.31e-04 | 16 |
| GO:0001510 | Liver | HCC | RNA methylation | 53/7958 | 83/18723 | 6.96e-05 | 6.29e-04 | 53 |
| GO:0080009 | Liver | HCC | mRNA methylation | 12/7958 | 16/18723 | 8.74e-03 | 3.40e-02 | 12 |
| GO:0016556 | Liver | HCC | mRNA modification | 18/7958 | 27/18723 | 9.75e-03 | 3.66e-02 | 18 |
| GO:0008380113 | Thyroid | PTC | RNA splicing | 273/5968 | 434/18723 | 4.44e-41 | 1.40e-37 | 273 |
| GO:1903311112 | Thyroid | PTC | regulation of mRNA metabolic process | 181/5968 | 288/18723 | 1.60e-27 | 5.94e-25 | 181 |
| GO:0050684112 | Thyroid | PTC | regulation of mRNA processing | 98/5968 | 137/18723 | 1.53e-21 | 3.10e-19 | 98 |
| GO:00311235 | Thyroid | PTC | RNA 3'-end processing | 65/5968 | 116/18723 | 6.24e-08 | 1.30e-06 | 65 |
| GO:00311245 | Thyroid | PTC | mRNA 3'-end processing | 40/5968 | 62/18723 | 1.28e-07 | 2.48e-06 | 40 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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 |
| Page: 1 |
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