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Gene: USP2 |
Gene summary for USP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | USP2 | Gene ID | 9099 |
| Gene name | ubiquitin specific peptidase 2 | |
| Gene Alias | UBP41 | |
| Cytomap | 11q23.3 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | O75604 |
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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 |
| 9099 | USP2 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.38e-02 | 1.18e-01 | -0.1954 |
| 9099 | USP2 | HTA11_696_2000001011 | Human | Colorectum | AD | 5.33e-06 | 2.05e-01 | -0.1464 |
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| 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 |
| ∗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:00181083 | Oral cavity | OSCC | peptidyl-tyrosine phosphorylation | 177/7305 | 375/18723 | 6.86e-04 | 3.83e-03 | 177 |
| GO:00017043 | Oral cavity | OSCC | formation of primary germ layer | 65/7305 | 121/18723 | 7.08e-04 | 3.90e-03 | 65 |
| GO:00071629 | Oral cavity | OSCC | negative regulation of cell adhesion | 145/7305 | 303/18723 | 9.95e-04 | 5.18e-03 | 145 |
| GO:00610996 | Oral cavity | OSCC | negative regulation of protein tyrosine kinase activity | 21/7305 | 31/18723 | 1.13e-03 | 5.75e-03 | 21 |
| GO:0050732 | Oral cavity | OSCC | negative regulation of peptidyl-tyrosine phosphorylation | 35/7305 | 59/18723 | 1.24e-03 | 6.23e-03 | 35 |
| GO:00071789 | Oral cavity | OSCC | transmembrane receptor protein serine/threonine kinase signaling pathway | 165/7305 | 355/18723 | 2.31e-03 | 1.02e-02 | 165 |
| GO:00703045 | Oral cavity | OSCC | positive regulation of stress-activated protein kinase signaling cascade | 66/7305 | 128/18723 | 2.58e-03 | 1.13e-02 | 66 |
| GO:00328744 | Oral cavity | OSCC | positive regulation of stress-activated MAPK cascade | 64/7305 | 126/18723 | 4.67e-03 | 1.87e-02 | 64 |
| GO:003432916 | Oral cavity | OSCC | cell junction assembly | 190/7305 | 420/18723 | 4.99e-03 | 1.96e-02 | 190 |
| GO:00706462 | Oral cavity | OSCC | protein modification by small protein removal | 77/7305 | 157/18723 | 6.55e-03 | 2.43e-02 | 77 |
| GO:0061097 | Oral cavity | OSCC | regulation of protein tyrosine kinase activity | 47/7305 | 90/18723 | 7.37e-03 | 2.73e-02 | 47 |
| GO:00434107 | Oral cavity | OSCC | positive regulation of MAPK cascade | 213/7305 | 480/18723 | 8.71e-03 | 3.16e-02 | 213 |
| GO:00165782 | Oral cavity | OSCC | histone deubiquitination | 15/7305 | 23/18723 | 9.84e-03 | 3.46e-02 | 15 |
| GO:00463301 | Oral cavity | OSCC | positive regulation of JNK cascade | 46/7305 | 89/18723 | 1.01e-02 | 3.50e-02 | 46 |
| GO:0051348110 | Oral cavity | LP | negative regulation of transferase activity | 106/4623 | 268/18723 | 4.60e-08 | 1.61e-06 | 106 |
| GO:000734614 | Oral cavity | LP | regulation of mitotic cell cycle | 163/4623 | 457/18723 | 7.64e-08 | 2.56e-06 | 163 |
| GO:001820513 | Oral cavity | LP | peptidyl-lysine modification | 136/4623 | 376/18723 | 3.64e-07 | 1.06e-05 | 136 |
| GO:0010563110 | Oral cavity | LP | negative regulation of phosphorus metabolic process | 153/4623 | 442/18723 | 1.47e-06 | 3.53e-05 | 153 |
| GO:004354312 | Oral cavity | LP | protein acylation | 93/4623 | 243/18723 | 1.65e-06 | 3.86e-05 | 93 |
| GO:0045936110 | Oral cavity | LP | negative regulation of phosphate metabolic process | 152/4623 | 441/18723 | 2.10e-06 | 4.77e-05 | 152 |
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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 |
| USP2 | SNV | Missense_Mutation | rs369164717 | c.1216N>T | p.Arg406Trp | p.R406W | O75604 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AN-A0G0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| USP2 | SNV | Missense_Mutation | novel | c.1354N>A | p.Glu452Lys | p.E452K | O75604 | protein_coding | tolerated(0.18) | benign(0.058) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| USP2 | SNV | Missense_Mutation | novel | c.1743G>A | p.Met581Ile | p.M581I | O75604 | protein_coding | tolerated(0.36) | benign(0.034) | TCGA-C5-A8XJ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | SD |
| USP2 | SNV | Missense_Mutation | rs756703374 | c.1688N>A | p.Arg563His | p.R563H | O75604 | protein_coding | deleterious(0) | possibly_damaging(0.665) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| USP2 | SNV | Missense_Mutation | rs748109847 | c.1498C>T | p.Leu500Phe | p.L500F | O75604 | protein_coding | deleterious(0) | benign(0.424) | TCGA-A6-6141-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fu | SD |
| USP2 | SNV | Missense_Mutation | novel | c.728N>G | p.Gln243Arg | p.Q243R | O75604 | protein_coding | tolerated(0.51) | benign(0.107) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| USP2 | SNV | Missense_Mutation | rs373153803 | c.524N>T | p.Thr175Met | p.T175M | O75604 | protein_coding | deleterious_low_confidence(0.03) | possibly_damaging(0.813) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| USP2 | SNV | Missense_Mutation | rs369895568 | c.704N>T | p.Thr235Met | p.T235M | O75604 | protein_coding | tolerated(0.11) | benign(0.003) | TCGA-AA-3972-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | PD |
| USP2 | SNV | Missense_Mutation | c.287C>T | p.Thr96Ile | p.T96I | O75604 | protein_coding | tolerated_low_confidence(0.23) | benign(0.282) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| USP2 | SNV | Missense_Mutation | c.626N>A | p.Ser209Tyr | p.S209Y | O75604 | protein_coding | deleterious_low_confidence(0.03) | benign(0.058) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
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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 |
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | QUINALIZARIN | QUINALIZARIN | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | THONZONIUM BROMIDE | THONZONIUM BROMIDE | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | DEPHOSTATIN | DEPHOSTATIN | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | SURAMIN | SURAMIN | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | CALMIDAZOLIUM CHLORIDE | CALMIDAZOLIUM CHLORIDE | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | ZAPRINAST | ZAPRINAST | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | GNF-PF-254 | CHEMBL461579 | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | JUGLONE | JUGLONE | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | SENNOSIDE B | SENNOSIDE B | ||
| 9099 | USP2 | DRUGGABLE GENOME, ENZYME, TRANSCRIPTION FACTOR, PROTEASE | ELLAGIC ACID | ELLAGIC ACID |
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