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Gene: UBR4 |
Gene summary for UBR4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | UBR4 | Gene ID | 23352 |
| Gene name | ubiquitin protein ligase E3 component n-recognin 4 | |
| Gene Alias | RBAF600 | |
| Cytomap | 1p36.13 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q5T4S7 |
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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 |
| 23352 | UBR4 | LZE2T | Human | Esophagus | ESCC | 1.92e-08 | 9.84e-01 | 0.082 |
| 23352 | UBR4 | LZE4T | Human | Esophagus | ESCC | 7.62e-10 | 3.29e-01 | 0.0811 |
| 23352 | UBR4 | LZE5T | Human | Esophagus | ESCC | 2.50e-04 | 3.46e-01 | 0.0514 |
| 23352 | UBR4 | LZE7T | Human | Esophagus | ESCC | 1.44e-22 | 9.20e-01 | 0.0667 |
| 23352 | UBR4 | LZE8T | Human | Esophagus | ESCC | 3.29e-09 | 3.89e-01 | 0.067 |
| 23352 | UBR4 | LZE20T | Human | Esophagus | ESCC | 2.11e-11 | 3.64e-01 | 0.0662 |
| 23352 | UBR4 | LZE22D1 | Human | Esophagus | HGIN | 7.90e-05 | 2.75e-01 | 0.0595 |
| 23352 | UBR4 | LZE22T | Human | Esophagus | ESCC | 2.25e-02 | 2.92e-01 | 0.068 |
| 23352 | UBR4 | LZE24T | Human | Esophagus | ESCC | 2.04e-22 | 5.92e-01 | 0.0596 |
| 23352 | UBR4 | LZE21T | Human | Esophagus | ESCC | 2.86e-09 | 5.12e-01 | 0.0655 |
| 23352 | UBR4 | LZE6T | Human | Esophagus | ESCC | 2.51e-05 | 4.35e-01 | 0.0845 |
| 23352 | UBR4 | P1T-E | Human | Esophagus | ESCC | 3.61e-14 | 6.12e-01 | 0.0875 |
| 23352 | UBR4 | P2T-E | Human | Esophagus | ESCC | 4.16e-34 | 5.82e-01 | 0.1177 |
| 23352 | UBR4 | P4T-E | Human | Esophagus | ESCC | 1.10e-10 | 3.36e-01 | 0.1323 |
| 23352 | UBR4 | P5T-E | Human | Esophagus | ESCC | 6.95e-12 | 2.60e-01 | 0.1327 |
| 23352 | UBR4 | P8T-E | Human | Esophagus | ESCC | 1.94e-27 | 5.14e-01 | 0.0889 |
| 23352 | UBR4 | P9T-E | Human | Esophagus | ESCC | 4.02e-18 | 3.86e-01 | 0.1131 |
| 23352 | UBR4 | P10T-E | Human | Esophagus | ESCC | 3.53e-35 | 6.35e-01 | 0.116 |
| 23352 | UBR4 | P11T-E | Human | Esophagus | ESCC | 1.28e-17 | 9.84e-01 | 0.1426 |
| 23352 | UBR4 | P12T-E | Human | Esophagus | ESCC | 1.15e-23 | 4.97e-01 | 0.1122 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa052039 | Esophagus | HGIN | Viral carcinogenesis | 53/1383 | 204/8465 | 2.58e-04 | 2.71e-03 | 2.15e-03 | 53 |
| hsa0520315 | Esophagus | HGIN | Viral carcinogenesis | 53/1383 | 204/8465 | 2.58e-04 | 2.71e-03 | 2.15e-03 | 53 |
| hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
| hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
| hsa0516515 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
| hsa0520335 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
| hsa05165 | Liver | Cirrhotic | Human papillomavirus infection | 124/2530 | 331/8465 | 1.55e-03 | 7.83e-03 | 4.83e-03 | 124 |
| hsa05203 | Liver | Cirrhotic | Viral carcinogenesis | 76/2530 | 204/8465 | 1.34e-02 | 4.20e-02 | 2.59e-02 | 76 |
| hsa051651 | Liver | Cirrhotic | Human papillomavirus infection | 124/2530 | 331/8465 | 1.55e-03 | 7.83e-03 | 4.83e-03 | 124 |
| hsa052031 | Liver | Cirrhotic | Viral carcinogenesis | 76/2530 | 204/8465 | 1.34e-02 | 4.20e-02 | 2.59e-02 | 76 |
| hsa051652 | Liver | HCC | Human papillomavirus infection | 188/4020 | 331/8465 | 3.34e-04 | 1.49e-03 | 8.29e-04 | 188 |
| hsa052032 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
| hsa051653 | Liver | HCC | Human papillomavirus infection | 188/4020 | 331/8465 | 3.34e-04 | 1.49e-03 | 8.29e-04 | 188 |
| hsa052033 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
| hsa051656 | Lung | IAC | Human papillomavirus infection | 71/1053 | 331/8465 | 1.88e-06 | 7.63e-05 | 5.06e-05 | 71 |
| hsa052034 | Lung | IAC | Viral carcinogenesis | 43/1053 | 204/8465 | 3.02e-04 | 3.07e-03 | 2.04e-03 | 43 |
| hsa0516511 | Lung | IAC | Human papillomavirus infection | 71/1053 | 331/8465 | 1.88e-06 | 7.63e-05 | 5.06e-05 | 71 |
| hsa0520311 | Lung | IAC | Viral carcinogenesis | 43/1053 | 204/8465 | 3.02e-04 | 3.07e-03 | 2.04e-03 | 43 |
| hsa0516521 | Lung | AIS | Human papillomavirus infection | 64/961 | 331/8465 | 1.03e-05 | 3.04e-04 | 1.95e-04 | 64 |
| hsa0520321 | Lung | AIS | Viral carcinogenesis | 37/961 | 204/8465 | 2.49e-03 | 1.49e-02 | 9.55e-03 | 37 |
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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 |
| UBR4 | SNV | Missense_Mutation | c.2370G>A | p.Met790Ile | p.M790I | Q5T4S7 | protein_coding | tolerated(0.09) | benign(0) | TCGA-A2-A0EU-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| UBR4 | SNV | Missense_Mutation | c.8743A>C | p.Ser2915Arg | p.S2915R | Q5T4S7 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-A2-A0T0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| UBR4 | SNV | Missense_Mutation | rs772692146 | c.7600N>C | p.Thr2534Pro | p.T2534P | Q5T4S7 | protein_coding | tolerated(0.21) | possibly_damaging(0.72) | TCGA-A2-A0YD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| UBR4 | SNV | Missense_Mutation | c.15224N>C | p.Gly5075Ala | p.G5075A | Q5T4S7 | protein_coding | tolerated(0.55) | benign(0.099) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| UBR4 | SNV | Missense_Mutation | novel | c.12940N>T | p.Ile4314Phe | p.I4314F | Q5T4S7 | protein_coding | deleterious(0) | benign(0.021) | TCGA-A2-A4RW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| UBR4 | SNV | Missense_Mutation | c.6962N>A | p.Leu2321Gln | p.L2321Q | Q5T4S7 | protein_coding | deleterious(0) | possibly_damaging(0.548) | TCGA-A8-A085-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| UBR4 | SNV | Missense_Mutation | rs555728639 | c.3617N>G | p.Ser1206Cys | p.S1206C | Q5T4S7 | protein_coding | deleterious(0.02) | probably_damaging(0.981) | TCGA-A8-A085-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| UBR4 | SNV | Missense_Mutation | c.12865G>A | p.Asp4289Asn | p.D4289N | Q5T4S7 | protein_coding | tolerated(0.05) | benign(0.001) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| UBR4 | SNV | Missense_Mutation | c.14108N>T | p.Lys4703Met | p.K4703M | Q5T4S7 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A8-A09W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| UBR4 | SNV | Missense_Mutation | c.4820N>T | p.Thr1607Met | p.T1607M | Q5T4S7 | protein_coding | tolerated(0.33) | benign(0.015) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| 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 34 35 36 37 38 39 40 41 42 43 |
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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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