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Gene: USP5 |
Gene summary for USP5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | USP5 | Gene ID | 8078 |
| Gene name | ubiquitin specific peptidase 5 | |
| Gene Alias | ISOT | |
| Cytomap | 12p13.31 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | A0A140VJZ1 |
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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 |
| 8078 | USP5 | HTA11_3410_2000001011 | Human | Colorectum | AD | 9.57e-04 | 1.56e-01 | 0.0155 |
| 8078 | USP5 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.92e-04 | 2.68e-01 | -0.1808 |
| 8078 | USP5 | HTA11_1938_2000001011 | Human | Colorectum | AD | 8.81e-10 | 4.33e-01 | -0.0811 |
| 8078 | USP5 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.10e-05 | 2.55e-01 | -0.1954 |
| 8078 | USP5 | HTA11_411_2000001011 | Human | Colorectum | SER | 5.24e-03 | 5.44e-01 | -0.2602 |
| 8078 | USP5 | HTA11_696_2000001011 | Human | Colorectum | AD | 4.25e-14 | 3.22e-01 | -0.1464 |
| 8078 | USP5 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.71e-08 | 2.37e-01 | -0.1001 |
| 8078 | USP5 | HTA11_1391_2000001011 | Human | Colorectum | AD | 5.43e-10 | 4.42e-01 | -0.059 |
| 8078 | USP5 | HTA11_6801_2000001011 | Human | Colorectum | SER | 1.18e-07 | 4.91e-01 | 0.0171 |
| 8078 | USP5 | HTA11_7696_3000711011 | Human | Colorectum | AD | 4.40e-15 | 4.24e-01 | 0.0674 |
| 8078 | USP5 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.05e-02 | 2.43e-01 | 0.0588 |
| 8078 | USP5 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.03e-26 | 4.74e-01 | 0.294 |
| 8078 | USP5 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 6.62e-03 | 9.44e-01 | 0.3487 |
| 8078 | USP5 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.57e-02 | 3.03e-01 | 0.281 |
| 8078 | USP5 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 8.28e-24 | 4.91e-01 | 0.3859 |
| 8078 | USP5 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.50e-08 | 2.94e-01 | 0.3005 |
| 8078 | USP5 | LZE4T | Human | Esophagus | ESCC | 9.29e-03 | 1.59e-01 | 0.0811 |
| 8078 | USP5 | LZE7T | Human | Esophagus | ESCC | 4.74e-04 | 3.83e-01 | 0.0667 |
| 8078 | USP5 | LZE8T | Human | Esophagus | ESCC | 1.12e-08 | 2.94e-01 | 0.067 |
| 8078 | USP5 | LZE24T | Human | Esophagus | ESCC | 3.28e-05 | 2.09e-01 | 0.0596 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| 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 |
| GO:190305218 | Oral cavity | LP | positive regulation of proteolysis involved in cellular protein catabolic process | 61/4623 | 133/18723 | 8.17e-08 | 2.72e-06 | 61 |
| GO:2000060110 | Oral cavity | LP | positive regulation of ubiquitin-dependent protein catabolic process | 49/4623 | 107/18723 | 1.57e-06 | 3.72e-05 | 49 |
| GO:005140218 | Oral cavity | LP | neuron apoptotic process | 91/4623 | 246/18723 | 1.07e-05 | 1.94e-04 | 91 |
| GO:000961215 | Oral cavity | LP | response to mechanical stimulus | 81/4623 | 216/18723 | 1.80e-05 | 3.09e-04 | 81 |
| GO:004340918 | Oral cavity | LP | negative regulation of MAPK cascade | 67/4623 | 180/18723 | 1.18e-04 | 1.40e-03 | 67 |
| GO:000647016 | Oral cavity | LP | protein dephosphorylation | 89/4623 | 281/18723 | 4.60e-03 | 2.93e-02 | 89 |
| GO:000647023 | Oral cavity | EOLP | protein dephosphorylation | 72/2218 | 281/18723 | 1.19e-10 | 1.35e-08 | 72 |
| GO:001631114 | Oral cavity | EOLP | dephosphorylation | 85/2218 | 417/18723 | 3.19e-07 | 9.47e-06 | 85 |
| GO:007099726 | Oral cavity | EOLP | neuron death | 70/2218 | 361/18723 | 2.01e-05 | 3.18e-04 | 70 |
| GO:004340924 | Oral cavity | EOLP | negative regulation of MAPK cascade | 39/2218 | 180/18723 | 1.25e-04 | 1.38e-03 | 39 |
| GO:003597011 | Oral cavity | EOLP | peptidyl-threonine dephosphorylation | 8/2218 | 16/18723 | 2.04e-04 | 2.05e-03 | 8 |
| GO:000736913 | Oral cavity | EOLP | gastrulation | 39/2218 | 185/18723 | 2.29e-04 | 2.25e-03 | 39 |
| GO:007064611 | Oral cavity | EOLP | protein modification by small protein removal | 33/2218 | 157/18723 | 7.04e-04 | 5.78e-03 | 33 |
| GO:000749212 | Oral cavity | EOLP | endoderm development | 19/2218 | 77/18723 | 1.32e-03 | 9.33e-03 | 19 |
| GO:005140224 | Oral cavity | EOLP | neuron apoptotic process | 45/2218 | 246/18723 | 1.96e-03 | 1.25e-02 | 45 |
| GO:00165792 | Oral cavity | EOLP | protein deubiquitination | 28/2218 | 139/18723 | 3.29e-03 | 1.90e-02 | 28 |
| GO:000170611 | Oral cavity | EOLP | endoderm formation | 14/2218 | 54/18723 | 3.37e-03 | 1.94e-02 | 14 |
| GO:000961223 | Oral cavity | EOLP | response to mechanical stimulus | 39/2218 | 216/18723 | 4.72e-03 | 2.54e-02 | 39 |
| GO:000170412 | Oral cavity | EOLP | formation of primary germ layer | 24/2218 | 121/18723 | 7.53e-03 | 3.62e-02 | 24 |
| GO:000749221 | Oral cavity | NEOLP | endoderm development | 22/2005 | 77/18723 | 1.19e-05 | 2.17e-04 | 22 |
| 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 |
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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 |
| USP5 | SNV | Missense_Mutation | c.103N>A | p.Asp35Asn | p.D35N | P45974 | protein_coding | deleterious(0.01) | benign(0.124) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| USP5 | SNV | Missense_Mutation | c.891N>C | p.Glu297Asp | p.E297D | P45974 | protein_coding | tolerated(0.09) | benign(0.031) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| USP5 | SNV | Missense_Mutation | rs782807103 | c.221G>A | p.Arg74Gln | p.R74Q | P45974 | protein_coding | tolerated(0.08) | benign(0.001) | TCGA-AN-A0G0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| USP5 | SNV | Missense_Mutation | c.1725N>T | p.Lys575Asn | p.K575N | P45974 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-BH-A0B4-01 | Breast | breast invasive carcinoma | Male | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| USP5 | SNV | Missense_Mutation | novel | c.334N>C | p.Glu112Gln | p.E112Q | P45974 | protein_coding | tolerated(0.37) | possibly_damaging(0.672) | TCGA-BH-A8FZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| USP5 | insertion | Frame_Shift_Ins | novel | c.339_340insGAAACCAGCCTGGGCAATATGGCAAGACCTCATC | p.Phe114GlufsTer13 | p.F114Efs*13 | P45974 | protein_coding | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| USP5 | insertion | Nonsense_Mutation | novel | c.480_481insCCATTCTGACCTCCTATTGGACTCAGTTTCTTTTTTTCACCTACT | p.Ala160_Ser161insProPheTerProProIleGlyLeuSerPhePhePheSerProThr | p.A160_S161insPF*PPIGLSFFFSPT | P45974 | protein_coding | TCGA-A8-A08Z-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| USP5 | deletion | Frame_Shift_Del | novel | c.851_852delNN | p.Leu284GlnfsTer11 | p.L284Qfs*11 | P45974 | protein_coding | TCGA-E9-A1RH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | SD | ||
| USP5 | deletion | Frame_Shift_Del | c.1931delN | p.Pro645LeufsTer45 | p.P645Lfs*45 | P45974 | protein_coding | TCGA-E9-A226-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | tamoxiphen | PD | |||
| USP5 | SNV | Missense_Mutation | novel | c.907N>T | p.Arg303Trp | p.R303W | P45974 | protein_coding | deleterious(0) | probably_damaging(0.999) | 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 10 11 |
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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 |
| 8078 | USP5 | ENZYME, PROTEASE | VIALININ A | VIALININ A | 23791076 | |
| 8078 | USP5 | ENZYME, PROTEASE | inhibitor | 252166869 |
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