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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 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:200123313 | Lung | AIS | regulation of apoptotic signaling pathway | 71/1849 | 356/18723 | 6.10e-09 | 9.87e-07 | 71 |
GO:003164713 | Lung | AIS | regulation of protein stability | 62/1849 | 298/18723 | 1.06e-08 | 1.63e-06 | 62 |
GO:001657012 | Lung | AIS | histone modification | 81/1849 | 463/18723 | 2.30e-07 | 2.16e-05 | 81 |
GO:006082812 | Lung | AIS | regulation of canonical Wnt signaling pathway | 52/1849 | 253/18723 | 2.40e-07 | 2.22e-05 | 52 |
GO:006007012 | Lung | AIS | canonical Wnt signaling pathway | 59/1849 | 303/18723 | 2.73e-07 | 2.37e-05 | 59 |
GO:001604912 | Lung | AIS | cell growth | 83/1849 | 482/18723 | 3.26e-07 | 2.79e-05 | 83 |
GO:200123413 | Lung | AIS | negative regulation of apoptotic signaling pathway | 46/1849 | 224/18723 | 1.19e-06 | 8.00e-05 | 46 |
GO:200124213 | Lung | AIS | regulation of intrinsic apoptotic signaling pathway | 37/1849 | 164/18723 | 1.26e-06 | 8.19e-05 | 37 |
GO:004477211 | Lung | AIS | mitotic cell cycle phase transition | 69/1849 | 424/18723 | 2.23e-05 | 7.42e-04 | 69 |
GO:200124313 | Lung | AIS | negative regulation of intrinsic apoptotic signaling pathway | 23/1849 | 98/18723 | 6.45e-05 | 1.74e-03 | 23 |
GO:000931411 | Lung | AIS | response to radiation | 71/1849 | 456/18723 | 7.33e-05 | 1.91e-03 | 71 |
GO:000838013 | Lung | AIS | RNA splicing | 68/1849 | 434/18723 | 8.50e-05 | 2.11e-03 | 68 |
GO:003017712 | Lung | AIS | positive regulation of Wnt signaling pathway | 29/1849 | 140/18723 | 9.01e-05 | 2.21e-03 | 29 |
GO:004592712 | Lung | AIS | positive regulation of growth | 44/1849 | 259/18723 | 2.48e-04 | 4.83e-03 | 44 |
GO:007147812 | Lung | AIS | cellular response to radiation | 34/1849 | 186/18723 | 3.06e-04 | 5.62e-03 | 34 |
GO:004586113 | Lung | AIS | negative regulation of proteolysis | 55/1849 | 351/18723 | 3.87e-04 | 6.72e-03 | 55 |
GO:005254713 | Lung | AIS | regulation of peptidase activity | 68/1849 | 461/18723 | 5.01e-04 | 8.23e-03 | 68 |
GO:000155812 | Lung | AIS | regulation of cell growth | 62/1849 | 414/18723 | 5.85e-04 | 9.03e-03 | 62 |
GO:009026312 | Lung | AIS | positive regulation of canonical Wnt signaling pathway | 22/1849 | 106/18723 | 5.91e-04 | 9.03e-03 | 22 |
GO:200102012 | Lung | AIS | regulation of response to DNA damage stimulus | 37/1849 | 219/18723 | 8.22e-04 | 1.14e-02 | 37 |
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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 |
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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. |
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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 |
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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 |
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