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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). |
| 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:00064753 | Prostate | BPH | internal protein amino acid acetylation | 40/3107 | 160/18723 | 4.17e-03 | 2.06e-02 | 40 |
| GO:00165781 | Prostate | BPH | histone deubiquitination | 9/3107 | 23/18723 | 8.32e-03 | 3.60e-02 | 9 |
| GO:19042921 | Prostate | BPH | regulation of ERAD pathway | 8/3107 | 20/18723 | 1.09e-02 | 4.50e-02 | 8 |
| GO:004217619 | Prostate | Tumor | regulation of protein catabolic process | 142/3246 | 391/18723 | 9.32e-20 | 5.79e-17 | 142 |
| GO:001049819 | Prostate | Tumor | proteasomal protein catabolic process | 158/3246 | 490/18723 | 3.05e-16 | 6.76e-14 | 158 |
| GO:003497619 | Prostate | Tumor | response to endoplasmic reticulum stress | 97/3246 | 256/18723 | 2.92e-15 | 4.78e-13 | 97 |
| GO:190336219 | Prostate | Tumor | regulation of cellular protein catabolic process | 95/3246 | 255/18723 | 1.92e-14 | 2.54e-12 | 95 |
| GO:190305019 | Prostate | Tumor | regulation of proteolysis involved in cellular protein catabolic process | 83/3246 | 221/18723 | 5.12e-13 | 5.49e-11 | 83 |
| GO:006113619 | Prostate | Tumor | regulation of proteasomal protein catabolic process | 71/3246 | 187/18723 | 1.34e-11 | 1.00e-09 | 71 |
| GO:004217718 | Prostate | Tumor | negative regulation of protein catabolic process | 49/3246 | 121/18723 | 1.53e-09 | 7.19e-08 | 49 |
| GO:000989518 | Prostate | Tumor | negative regulation of catabolic process | 96/3246 | 320/18723 | 1.40e-08 | 5.07e-07 | 96 |
| GO:004586119 | Prostate | Tumor | negative regulation of proteolysis | 102/3246 | 351/18723 | 3.09e-08 | 9.94e-07 | 102 |
| GO:003133019 | Prostate | Tumor | negative regulation of cellular catabolic process | 81/3246 | 262/18723 | 4.42e-08 | 1.37e-06 | 81 |
| GO:001657013 | Prostate | Tumor | histone modification | 126/3246 | 463/18723 | 5.51e-08 | 1.65e-06 | 126 |
| GO:190589719 | Prostate | Tumor | regulation of response to endoplasmic reticulum stress | 35/3246 | 82/18723 | 6.76e-08 | 1.95e-06 | 35 |
| GO:190336316 | Prostate | Tumor | negative regulation of cellular protein catabolic process | 32/3246 | 75/18723 | 2.47e-07 | 5.72e-06 | 32 |
| GO:190305116 | Prostate | Tumor | negative regulation of proteolysis involved in cellular protein catabolic process | 28/3246 | 64/18723 | 7.39e-07 | 1.47e-05 | 28 |
| GO:190357318 | Prostate | Tumor | negative regulation of response to endoplasmic reticulum stress | 21/3246 | 44/18723 | 3.25e-06 | 5.31e-05 | 21 |
| GO:001820512 | Prostate | Tumor | peptidyl-lysine modification | 99/3246 | 376/18723 | 6.77e-06 | 1.02e-04 | 99 |
| GO:001839411 | Prostate | Tumor | peptidyl-lysine acetylation | 52/3246 | 169/18723 | 1.25e-05 | 1.76e-04 | 52 |
| 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 |
| 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. |
| 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 |
| 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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