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Gene: RNF4 |
Gene summary for RNF4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RNF4 | Gene ID | 6047 |
| Gene name | ring finger protein 4 | |
| Gene Alias | RES4-26 | |
| Cytomap | 4p16.3 | |
| Gene Type | protein-coding | GO ID | GO:0000209 | UniProtAcc | P78317 |
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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 |
| 6047 | RNF4 | LZE4T | Human | Esophagus | ESCC | 1.06e-03 | 4.70e-02 | 0.0811 |
| 6047 | RNF4 | LZE7T | Human | Esophagus | ESCC | 1.79e-06 | 6.06e-01 | 0.0667 |
| 6047 | RNF4 | LZE24T | Human | Esophagus | ESCC | 5.58e-06 | 2.11e-01 | 0.0596 |
| 6047 | RNF4 | LZE6T | Human | Esophagus | ESCC | 3.56e-04 | 3.09e-01 | 0.0845 |
| 6047 | RNF4 | P1T-E | Human | Esophagus | ESCC | 3.92e-04 | 3.08e-01 | 0.0875 |
| 6047 | RNF4 | P2T-E | Human | Esophagus | ESCC | 7.37e-23 | 4.55e-01 | 0.1177 |
| 6047 | RNF4 | P4T-E | Human | Esophagus | ESCC | 3.39e-16 | 2.42e-01 | 0.1323 |
| 6047 | RNF4 | P5T-E | Human | Esophagus | ESCC | 2.51e-09 | 2.04e-01 | 0.1327 |
| 6047 | RNF4 | P8T-E | Human | Esophagus | ESCC | 9.00e-19 | 4.46e-01 | 0.0889 |
| 6047 | RNF4 | P9T-E | Human | Esophagus | ESCC | 1.37e-08 | 1.04e-01 | 0.1131 |
| 6047 | RNF4 | P10T-E | Human | Esophagus | ESCC | 1.20e-17 | 2.72e-01 | 0.116 |
| 6047 | RNF4 | P11T-E | Human | Esophagus | ESCC | 2.03e-10 | 2.98e-01 | 0.1426 |
| 6047 | RNF4 | P12T-E | Human | Esophagus | ESCC | 5.09e-09 | 2.75e-01 | 0.1122 |
| 6047 | RNF4 | P15T-E | Human | Esophagus | ESCC | 7.41e-10 | 1.34e-01 | 0.1149 |
| 6047 | RNF4 | P16T-E | Human | Esophagus | ESCC | 1.40e-14 | 2.95e-01 | 0.1153 |
| 6047 | RNF4 | P17T-E | Human | Esophagus | ESCC | 1.50e-06 | 3.66e-01 | 0.1278 |
| 6047 | RNF4 | P19T-E | Human | Esophagus | ESCC | 7.54e-04 | 4.16e-01 | 0.1662 |
| 6047 | RNF4 | P20T-E | Human | Esophagus | ESCC | 5.19e-19 | 2.66e-01 | 0.1124 |
| 6047 | RNF4 | P21T-E | Human | Esophagus | ESCC | 1.36e-09 | 1.52e-01 | 0.1617 |
| 6047 | RNF4 | P22T-E | Human | Esophagus | ESCC | 3.12e-21 | 1.73e-01 | 0.1236 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:001049820 | Oral cavity | OSCC | proteasomal protein catabolic process | 336/7305 | 490/18723 | 5.45e-41 | 8.63e-38 | 336 |
| GO:004316120 | Oral cavity | OSCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 285/7305 | 412/18723 | 5.68e-36 | 5.99e-33 | 285 |
| GO:000989620 | Oral cavity | OSCC | positive regulation of catabolic process | 307/7305 | 492/18723 | 2.29e-26 | 7.64e-24 | 307 |
| GO:003133120 | Oral cavity | OSCC | positive regulation of cellular catabolic process | 273/7305 | 427/18723 | 6.39e-26 | 2.02e-23 | 273 |
| GO:004217620 | Oral cavity | OSCC | regulation of protein catabolic process | 254/7305 | 391/18723 | 1.07e-25 | 3.22e-23 | 254 |
| GO:190331118 | Oral cavity | OSCC | regulation of mRNA metabolic process | 197/7305 | 288/18723 | 2.83e-24 | 7.16e-22 | 197 |
| GO:004586220 | Oral cavity | OSCC | positive regulation of proteolysis | 236/7305 | 372/18723 | 6.53e-22 | 1.38e-19 | 236 |
| GO:190336220 | Oral cavity | OSCC | regulation of cellular protein catabolic process | 174/7305 | 255/18723 | 2.04e-21 | 3.70e-19 | 174 |
| GO:190332020 | Oral cavity | OSCC | regulation of protein modification by small protein conjugation or removal | 165/7305 | 242/18723 | 2.52e-20 | 3.99e-18 | 165 |
| GO:190305020 | Oral cavity | OSCC | regulation of proteolysis involved in cellular protein catabolic process | 152/7305 | 221/18723 | 2.16e-19 | 3.15e-17 | 152 |
| GO:005068417 | Oral cavity | OSCC | regulation of mRNA processing | 104/7305 | 137/18723 | 1.32e-18 | 1.58e-16 | 104 |
| GO:006113620 | Oral cavity | OSCC | regulation of proteasomal protein catabolic process | 132/7305 | 187/18723 | 1.57e-18 | 1.81e-16 | 132 |
| GO:004325420 | Oral cavity | OSCC | regulation of protein-containing complex assembly | 255/7305 | 428/18723 | 2.94e-18 | 3.15e-16 | 255 |
| GO:003139620 | Oral cavity | OSCC | regulation of protein ubiquitination | 143/7305 | 210/18723 | 1.01e-17 | 9.80e-16 | 143 |
| GO:00165707 | Oral cavity | OSCC | histone modification | 270/7305 | 463/18723 | 1.59e-17 | 1.50e-15 | 270 |
| GO:004573220 | Oral cavity | OSCC | positive regulation of protein catabolic process | 150/7305 | 231/18723 | 1.06e-15 | 7.64e-14 | 150 |
| GO:009719120 | Oral cavity | OSCC | extrinsic apoptotic signaling pathway | 142/7305 | 219/18723 | 7.34e-15 | 4.55e-13 | 142 |
| GO:000020910 | Oral cavity | OSCC | protein polyubiquitination | 150/7305 | 236/18723 | 1.59e-14 | 9.27e-13 | 150 |
| GO:00330448 | Oral cavity | OSCC | regulation of chromosome organization | 123/7305 | 187/18723 | 9.87e-14 | 5.17e-12 | 123 |
| GO:190336420 | Oral cavity | OSCC | positive regulation of cellular protein catabolic process | 106/7305 | 155/18723 | 1.07e-13 | 5.53e-12 | 106 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| 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 |
| RNF4 | SNV | Missense_Mutation | rs201229382 | c.361N>A | p.Ala121Thr | p.A121T | P78317 | protein_coding | tolerated(0.62) | benign(0) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RNF4 | SNV | Missense_Mutation | rs377313523 | c.491N>A | p.Arg164His | p.R164H | P78317 | protein_coding | tolerated(0.08) | benign(0.08) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RNF4 | SNV | Missense_Mutation | c.423G>T | p.Glu141Asp | p.E141D | P78317 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RNF4 | SNV | Missense_Mutation | novel | c.346N>A | p.Ala116Thr | p.A116T | P78317 | protein_coding | tolerated(0.79) | benign(0) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RNF4 | SNV | Missense_Mutation | rs767261720 | c.448G>A | p.Val150Ile | p.V150I | P78317 | protein_coding | tolerated(0.08) | benign(0.026) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RNF4 | SNV | Missense_Mutation | rs750844745 | c.490N>T | p.Arg164Cys | p.R164C | P78317 | protein_coding | tolerated(0.16) | benign(0.035) | TCGA-D1-A167-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RNF4 | SNV | Missense_Mutation | novel | c.311N>A | p.Arg104Lys | p.R104K | P78317 | protein_coding | tolerated(0.6) | benign(0) | TCGA-FI-A2D0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RNF4 | SNV | Missense_Mutation | novel | c.467N>G | p.His156Arg | p.H156R | P78317 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RNF4 | SNV | Missense_Mutation | c.421N>A | p.Glu141Lys | p.E141K | P78317 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-MT-A67F-01 | Oral cavity | head & neck squamous cell carcinoma | 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 |
| Page: 1 |
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