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Gene: USP4 |
Gene summary for USP4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | USP4 | Gene ID | 7375 |
| Gene name | ubiquitin specific peptidase 4 | |
| Gene Alias | UNP | |
| Cytomap | 3p21.31 | |
| Gene Type | protein-coding | GO ID | GO:0000244 | UniProtAcc | Q13107 |
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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 |
| 7375 | USP4 | LZE4T | Human | Esophagus | ESCC | 4.63e-13 | 3.22e-01 | 0.0811 |
| 7375 | USP4 | LZE7T | Human | Esophagus | ESCC | 2.43e-04 | 2.85e-01 | 0.0667 |
| 7375 | USP4 | LZE8T | Human | Esophagus | ESCC | 1.96e-03 | 9.50e-02 | 0.067 |
| 7375 | USP4 | LZE22T | Human | Esophagus | ESCC | 2.12e-05 | 3.91e-01 | 0.068 |
| 7375 | USP4 | LZE24T | Human | Esophagus | ESCC | 2.95e-14 | 2.93e-01 | 0.0596 |
| 7375 | USP4 | P1T-E | Human | Esophagus | ESCC | 6.26e-04 | 2.28e-01 | 0.0875 |
| 7375 | USP4 | P2T-E | Human | Esophagus | ESCC | 1.34e-18 | 3.51e-01 | 0.1177 |
| 7375 | USP4 | P4T-E | Human | Esophagus | ESCC | 1.89e-21 | 4.95e-01 | 0.1323 |
| 7375 | USP4 | P5T-E | Human | Esophagus | ESCC | 6.58e-12 | 2.21e-01 | 0.1327 |
| 7375 | USP4 | P8T-E | Human | Esophagus | ESCC | 9.77e-09 | 1.99e-01 | 0.0889 |
| 7375 | USP4 | P9T-E | Human | Esophagus | ESCC | 1.11e-12 | 3.07e-01 | 0.1131 |
| 7375 | USP4 | P10T-E | Human | Esophagus | ESCC | 9.81e-23 | 4.08e-01 | 0.116 |
| 7375 | USP4 | P11T-E | Human | Esophagus | ESCC | 7.00e-16 | 5.24e-01 | 0.1426 |
| 7375 | USP4 | P12T-E | Human | Esophagus | ESCC | 4.56e-21 | 4.02e-01 | 0.1122 |
| 7375 | USP4 | P15T-E | Human | Esophagus | ESCC | 1.17e-16 | 3.22e-01 | 0.1149 |
| 7375 | USP4 | P16T-E | Human | Esophagus | ESCC | 1.63e-18 | 4.47e-01 | 0.1153 |
| 7375 | USP4 | P17T-E | Human | Esophagus | ESCC | 1.31e-02 | 2.80e-01 | 0.1278 |
| 7375 | USP4 | P19T-E | Human | Esophagus | ESCC | 2.52e-06 | 6.24e-01 | 0.1662 |
| 7375 | USP4 | P20T-E | Human | Esophagus | ESCC | 8.87e-20 | 4.24e-01 | 0.1124 |
| 7375 | USP4 | P21T-E | Human | Esophagus | ESCC | 1.20e-18 | 3.57e-01 | 0.1617 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:007121412 | Lung | AIS | cellular response to abiotic stimulus | 51/1849 | 331/18723 | 9.10e-04 | 1.21e-02 | 51 |
| GO:010400412 | Lung | AIS | cellular response to environmental stimulus | 51/1849 | 331/18723 | 9.10e-04 | 1.21e-02 | 51 |
| GO:005254813 | Lung | AIS | regulation of endopeptidase activity | 63/1849 | 432/18723 | 1.06e-03 | 1.38e-02 | 63 |
| GO:000037713 | Lung | AIS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 49/1849 | 320/18723 | 1.30e-03 | 1.63e-02 | 49 |
| GO:000039813 | Lung | AIS | mRNA splicing, via spliceosome | 49/1849 | 320/18723 | 1.30e-03 | 1.63e-02 | 49 |
| GO:004328113 | Lung | AIS | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 35/1849 | 209/18723 | 1.31e-03 | 1.63e-02 | 35 |
| GO:000863012 | Lung | AIS | intrinsic apoptotic signaling pathway in response to DNA damage | 20/1849 | 99/18723 | 1.46e-03 | 1.77e-02 | 20 |
| GO:200011613 | Lung | AIS | regulation of cysteine-type endopeptidase activity | 38/1849 | 235/18723 | 1.62e-03 | 1.87e-02 | 38 |
| GO:000037513 | Lung | AIS | RNA splicing, via transesterification reactions | 49/1849 | 324/18723 | 1.69e-03 | 1.93e-02 | 49 |
| GO:003030712 | Lung | AIS | positive regulation of cell growth | 29/1849 | 166/18723 | 1.70e-03 | 1.93e-02 | 29 |
| GO:190222911 | Lung | AIS | regulation of intrinsic apoptotic signaling pathway in response to DNA damage | 10/1849 | 36/18723 | 1.98e-03 | 2.18e-02 | 10 |
| GO:00094162 | Lung | AIS | response to light stimulus | 47/1849 | 320/18723 | 3.72e-03 | 3.48e-02 | 47 |
| GO:20010211 | Lung | AIS | negative regulation of response to DNA damage stimulus | 16/1849 | 81/18723 | 5.23e-03 | 4.49e-02 | 16 |
| GO:000838023 | Lung | MIAC | RNA splicing | 44/967 | 434/18723 | 1.56e-05 | 1.07e-03 | 44 |
| GO:001657022 | Lung | MIAC | histone modification | 45/967 | 463/18723 | 3.58e-05 | 1.97e-03 | 45 |
| GO:000037723 | Lung | MIAC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 33/967 | 320/18723 | 1.27e-04 | 5.13e-03 | 33 |
| GO:000039823 | Lung | MIAC | mRNA splicing, via spliceosome | 33/967 | 320/18723 | 1.27e-04 | 5.13e-03 | 33 |
| GO:000037523 | Lung | MIAC | RNA splicing, via transesterification reactions | 33/967 | 324/18723 | 1.61e-04 | 6.19e-03 | 33 |
| GO:200123320 | Oral cavity | OSCC | regulation of apoptotic signaling pathway | 242/7305 | 356/18723 | 6.66e-29 | 3.24e-26 | 242 |
| GO:009719320 | Oral cavity | OSCC | intrinsic apoptotic signaling pathway | 202/7305 | 288/18723 | 4.64e-27 | 1.73e-24 | 202 |
| 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 44 45 46 47 48 49 50 51 |
| 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 |
| USP4 | SNV | Missense_Mutation | c.290N>A | p.Pro97His | p.P97H | Q13107 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD | |
| USP4 | SNV | Missense_Mutation | novel | c.1675C>T | p.Arg559Trp | p.R559W | Q13107 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-AC-A2QI-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | CR |
| USP4 | SNV | Missense_Mutation | c.944C>G | p.Ser315Cys | p.S315C | Q13107 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AR-A0TX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| USP4 | SNV | Missense_Mutation | novel | c.884N>G | p.Ser295Cys | p.S295C | Q13107 | protein_coding | tolerated(0.17) | possibly_damaging(0.566) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| USP4 | SNV | Missense_Mutation | novel | c.542N>A | p.Thr181Lys | p.T181K | Q13107 | protein_coding | deleterious(0) | possibly_damaging(0.788) | TCGA-C8-A3M8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | CR |
| USP4 | SNV | Missense_Mutation | c.241N>G | p.Gln81Glu | p.Q81E | Q13107 | protein_coding | tolerated(0.27) | possibly_damaging(0.633) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| USP4 | SNV | Missense_Mutation | novel | c.23N>A | p.Arg8His | p.R8H | Q13107 | protein_coding | tolerated_low_confidence(0.16) | benign(0) | TCGA-E9-A54X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| USP4 | insertion | Frame_Shift_Ins | novel | c.2080_2081insTTTGTATTTGGATGTGTCACTTCTT | p.Gln694LeufsTer34 | p.Q694Lfs*34 | Q13107 | protein_coding | TCGA-B6-A0RG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| USP4 | deletion | Frame_Shift_Del | novel | c.1830delN | p.Lys611SerfsTer4 | p.K611Sfs*4 | Q13107 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| USP4 | SNV | Missense_Mutation | rs148734128 | c.2204G>A | p.Arg735Gln | p.R735Q | Q13107 | protein_coding | tolerated(0.8) | benign(0.063) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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