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Gene: USP4 |
Gene summary for USP4 |
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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 |
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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 |
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∗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 |
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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 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00703713 | Breast | IDC | ERK1 and ERK2 cascade | 43/1434 | 330/18723 | 4.28e-04 | 5.84e-03 | 43 |
GO:00703733 | Breast | IDC | negative regulation of ERK1 and ERK2 cascade | 14/1434 | 78/18723 | 2.21e-03 | 2.06e-02 | 14 |
GO:00703722 | Breast | IDC | regulation of ERK1 and ERK2 cascade | 37/1434 | 309/18723 | 4.53e-03 | 3.49e-02 | 37 |
GO:007037111 | Breast | DCIS | ERK1 and ERK2 cascade | 41/1390 | 330/18723 | 8.11e-04 | 9.32e-03 | 41 |
GO:007037311 | Breast | DCIS | negative regulation of ERK1 and ERK2 cascade | 14/1390 | 78/18723 | 1.65e-03 | 1.64e-02 | 14 |
GO:009719310 | Cervix | CC | intrinsic apoptotic signaling pathway | 85/2311 | 288/18723 | 4.56e-15 | 6.46e-12 | 85 |
GO:200123310 | Cervix | CC | regulation of apoptotic signaling pathway | 96/2311 | 356/18723 | 4.08e-14 | 3.05e-11 | 96 |
GO:005254710 | Cervix | CC | regulation of peptidase activity | 112/2311 | 461/18723 | 6.70e-13 | 3.08e-10 | 112 |
GO:005254810 | Cervix | CC | regulation of endopeptidase activity | 103/2311 | 432/18723 | 1.89e-11 | 5.14e-09 | 103 |
GO:200124210 | Cervix | CC | regulation of intrinsic apoptotic signaling pathway | 52/2311 | 164/18723 | 5.06e-11 | 1.01e-08 | 52 |
GO:00160557 | Cervix | CC | Wnt signaling pathway | 98/2311 | 444/18723 | 4.82e-09 | 4.65e-07 | 98 |
GO:01987387 | Cervix | CC | cell-cell signaling by wnt | 98/2311 | 446/18723 | 6.16e-09 | 5.58e-07 | 98 |
GO:200011610 | Cervix | CC | regulation of cysteine-type endopeptidase activity | 61/2311 | 235/18723 | 8.69e-09 | 7.22e-07 | 61 |
GO:004328110 | Cervix | CC | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 55/2311 | 209/18723 | 2.77e-08 | 1.95e-06 | 55 |
GO:004586110 | Cervix | CC | negative regulation of proteolysis | 80/2311 | 351/18723 | 2.88e-08 | 1.98e-06 | 80 |
GO:00301117 | Cervix | CC | regulation of Wnt signaling pathway | 76/2311 | 328/18723 | 3.05e-08 | 2.08e-06 | 76 |
GO:200123410 | Cervix | CC | negative regulation of apoptotic signaling pathway | 56/2311 | 224/18723 | 1.39e-07 | 6.70e-06 | 56 |
GO:00447725 | Cervix | CC | mitotic cell cycle phase transition | 89/2311 | 424/18723 | 2.70e-07 | 1.12e-05 | 89 |
GO:00513469 | Cervix | CC | negative regulation of hydrolase activity | 81/2311 | 379/18723 | 4.27e-07 | 1.67e-05 | 81 |
GO:00104669 | Cervix | CC | negative regulation of peptidase activity | 60/2311 | 262/18723 | 1.27e-06 | 4.34e-05 | 60 |
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 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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. |
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Somatic mutation of malignant transformation related genes |
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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 | rs760275117 | c.1606N>A | p.Ala536Thr | p.A536T | Q13107 | protein_coding | tolerated(1) | benign(0.001) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
USP4 | SNV | Missense_Mutation | c.1750N>G | p.Phe584Val | p.F584V | Q13107 | protein_coding | tolerated(0.05) | benign(0.105) | TCGA-CM-6162-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
USP4 | SNV | Missense_Mutation | c.910N>T | p.Leu304Phe | p.L304F | Q13107 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D5-6533-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | oxaliplatin | CR | |
USP4 | SNV | Missense_Mutation | c.896N>A | p.Pro299His | p.P299H | Q13107 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
USP4 | SNV | Missense_Mutation | c.2162N>T | p.Asn721Ile | p.N721I | Q13107 | protein_coding | tolerated(0.08) | benign(0.038) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
USP4 | SNV | Missense_Mutation | c.1306N>C | p.Trp436Arg | p.W436R | Q13107 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
USP4 | SNV | Missense_Mutation | novel | c.1719N>A | p.Asp573Glu | p.D573E | Q13107 | protein_coding | tolerated(1) | benign(0.006) | TCGA-AG-A023-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
USP4 | SNV | Missense_Mutation | novel | c.2302N>T | p.Pro768Ser | p.P768S | Q13107 | protein_coding | tolerated(0.16) | benign(0.216) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
USP4 | SNV | Missense_Mutation | rs769716688 | c.2768N>A | p.Arg923Gln | p.R923Q | Q13107 | protein_coding | tolerated(0.93) | benign(0.007) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
USP4 | SNV | Missense_Mutation | rs546430537 | c.1102N>A | p.Ala368Thr | p.A368T | Q13107 | protein_coding | tolerated(0.52) | benign(0) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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