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Gene: RNF2 |
Gene summary for RNF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RNF2 | Gene ID | 6045 |
| Gene name | ring finger protein 2 | |
| Gene Alias | BAP-1 | |
| Cytomap | 1q25.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q99496 |
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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 |
| 6045 | RNF2 | LZE4T | Human | Esophagus | ESCC | 7.12e-03 | 1.03e-01 | 0.0811 |
| 6045 | RNF2 | LZE8T | Human | Esophagus | ESCC | 2.48e-08 | 1.41e-01 | 0.067 |
| 6045 | RNF2 | LZE24T | Human | Esophagus | ESCC | 2.31e-19 | 3.44e-01 | 0.0596 |
| 6045 | RNF2 | LZE6T | Human | Esophagus | ESCC | 1.67e-02 | 1.92e-01 | 0.0845 |
| 6045 | RNF2 | P1T-E | Human | Esophagus | ESCC | 6.43e-03 | 2.00e-01 | 0.0875 |
| 6045 | RNF2 | P2T-E | Human | Esophagus | ESCC | 9.00e-29 | 4.63e-01 | 0.1177 |
| 6045 | RNF2 | P4T-E | Human | Esophagus | ESCC | 4.16e-15 | 3.56e-01 | 0.1323 |
| 6045 | RNF2 | P5T-E | Human | Esophagus | ESCC | 1.20e-23 | 5.29e-01 | 0.1327 |
| 6045 | RNF2 | P8T-E | Human | Esophagus | ESCC | 1.32e-14 | 1.75e-01 | 0.0889 |
| 6045 | RNF2 | P9T-E | Human | Esophagus | ESCC | 3.02e-16 | 2.91e-01 | 0.1131 |
| 6045 | RNF2 | P10T-E | Human | Esophagus | ESCC | 1.95e-21 | 4.38e-01 | 0.116 |
| 6045 | RNF2 | P11T-E | Human | Esophagus | ESCC | 3.36e-09 | 4.31e-01 | 0.1426 |
| 6045 | RNF2 | P12T-E | Human | Esophagus | ESCC | 1.45e-06 | 2.82e-01 | 0.1122 |
| 6045 | RNF2 | P15T-E | Human | Esophagus | ESCC | 9.35e-24 | 5.15e-01 | 0.1149 |
| 6045 | RNF2 | P16T-E | Human | Esophagus | ESCC | 7.63e-31 | 5.73e-01 | 0.1153 |
| 6045 | RNF2 | P17T-E | Human | Esophagus | ESCC | 7.75e-05 | 3.14e-01 | 0.1278 |
| 6045 | RNF2 | P19T-E | Human | Esophagus | ESCC | 1.31e-02 | 4.86e-01 | 0.1662 |
| 6045 | RNF2 | P20T-E | Human | Esophagus | ESCC | 9.47e-22 | 4.39e-01 | 0.1124 |
| 6045 | RNF2 | P21T-E | Human | Esophagus | ESCC | 2.43e-19 | 2.73e-01 | 0.1617 |
| 6045 | RNF2 | P22T-E | Human | Esophagus | ESCC | 3.54e-13 | 2.73e-01 | 0.1236 |
| Page: 1 2 3 4 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:001657413 | Oral cavity | LP | histone ubiquitination | 22/4623 | 47/18723 | 8.02e-04 | 7.05e-03 | 22 |
| GO:001692511 | Oral cavity | LP | protein sumoylation | 24/4623 | 53/18723 | 8.55e-04 | 7.45e-03 | 24 |
| GO:00103901 | Oral cavity | LP | histone monoubiquitination | 15/4623 | 29/18723 | 1.55e-03 | 1.20e-02 | 15 |
| GO:007097911 | Oral cavity | LP | protein K11-linked ubiquitination | 15/4623 | 29/18723 | 1.55e-03 | 1.20e-02 | 15 |
| GO:005186512 | Oral cavity | LP | protein autoubiquitination | 29/4623 | 73/18723 | 3.20e-03 | 2.18e-02 | 29 |
| GO:006082815 | Oral cavity | LP | regulation of canonical Wnt signaling pathway | 82/4623 | 253/18723 | 3.23e-03 | 2.18e-02 | 82 |
| GO:003011115 | Oral cavity | LP | regulation of Wnt signaling pathway | 103/4623 | 328/18723 | 3.29e-03 | 2.21e-02 | 103 |
| GO:005077711 | Oral cavity | LP | negative regulation of immune response | 65/4623 | 194/18723 | 3.47e-03 | 2.32e-02 | 65 |
| GO:003352212 | Oral cavity | LP | histone H2A ubiquitination | 13/4623 | 26/18723 | 4.62e-03 | 2.93e-02 | 13 |
| GO:00506881 | Oral cavity | LP | regulation of defense response to virus | 27/4623 | 69/18723 | 5.55e-03 | 3.35e-02 | 27 |
| GO:004828511 | Oral cavity | LP | organelle fission | 145/4623 | 488/18723 | 6.02e-03 | 3.57e-02 | 145 |
| GO:009026315 | Oral cavity | LP | positive regulation of canonical Wnt signaling pathway | 38/4623 | 106/18723 | 6.67e-03 | 3.89e-02 | 38 |
| GO:0043433 | Oral cavity | LP | negative regulation of DNA-binding transcription factor activity | 61/4623 | 185/18723 | 6.68e-03 | 3.89e-02 | 61 |
| GO:000268315 | Oral cavity | LP | negative regulation of immune system process | 130/4623 | 434/18723 | 6.70e-03 | 3.90e-02 | 130 |
| GO:00988131 | Oral cavity | LP | nuclear chromosome segregation | 88/4623 | 281/18723 | 6.72e-03 | 3.91e-02 | 88 |
| GO:006007015 | Oral cavity | LP | canonical Wnt signaling pathway | 94/4623 | 303/18723 | 6.97e-03 | 3.96e-02 | 94 |
| GO:007093622 | Oral cavity | EOLP | protein K48-linked ubiquitination | 31/2218 | 65/18723 | 9.08e-13 | 2.27e-10 | 31 |
| GO:001049825 | Oral cavity | EOLP | proteasomal protein catabolic process | 108/2218 | 490/18723 | 7.79e-11 | 9.51e-09 | 108 |
| GO:000283121 | Oral cavity | EOLP | regulation of response to biotic stimulus | 80/2218 | 327/18723 | 1.31e-10 | 1.43e-08 | 80 |
| GO:000020923 | Oral cavity | EOLP | protein polyubiquitination | 62/2218 | 236/18723 | 7.88e-10 | 5.90e-08 | 62 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 |
| 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 |
| RNF2 | SNV | Missense_Mutation | novel | c.848N>C | p.Leu283Pro | p.L283P | Q99496 | protein_coding | deleterious(0.02) | possibly_damaging(0.799) | TCGA-A2-A0EO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| RNF2 | SNV | Missense_Mutation | c.473G>A | p.Arg158Gln | p.R158Q | Q99496 | protein_coding | deleterious(0.01) | possibly_damaging(0.726) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RNF2 | SNV | Missense_Mutation | c.128G>A | p.Arg43Gln | p.R43Q | Q99496 | protein_coding | deleterious(0) | possibly_damaging(0.759) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RNF2 | SNV | Missense_Mutation | novel | c.293G>T | p.Arg98Ile | p.R98I | Q99496 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RNF2 | SNV | Missense_Mutation | c.577A>T | p.Ser193Cys | p.S193C | Q99496 | protein_coding | deleterious(0.02) | benign(0.015) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RNF2 | SNV | Missense_Mutation | novel | c.339N>G | p.Ile113Met | p.I113M | Q99496 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| RNF2 | SNV | Missense_Mutation | c.587G>A | p.Arg196Gln | p.R196Q | Q99496 | protein_coding | tolerated(0.13) | benign(0.003) | TCGA-CM-6674-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RNF2 | SNV | Missense_Mutation | c.77G>A | p.Arg26Gln | p.R26Q | Q99496 | protein_coding | deleterious(0.04) | possibly_damaging(0.688) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RNF2 | SNV | Missense_Mutation | c.77N>A | p.Arg26Gln | p.R26Q | Q99496 | protein_coding | deleterious(0.04) | possibly_damaging(0.688) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD | |
| RNF2 | insertion | Frame_Shift_Ins | novel | c.971_972insA | p.Met325HisfsTer16 | p.M325Hfs*16 | Q99496 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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