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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:006113622 | Liver | HCC | regulation of proteasomal protein catabolic process | 134/7958 | 187/18723 | 5.03e-16 | 4.09e-14 | 134 |
| GO:00182052 | Liver | HCC | peptidyl-lysine modification | 230/7958 | 376/18723 | 1.51e-13 | 8.32e-12 | 230 |
| GO:00064732 | Liver | HCC | protein acetylation | 135/7958 | 201/18723 | 1.20e-12 | 5.92e-11 | 135 |
| GO:00435432 | Liver | HCC | protein acylation | 157/7958 | 243/18723 | 2.40e-12 | 1.12e-10 | 157 |
| GO:001056322 | Liver | HCC | negative regulation of phosphorus metabolic process | 259/7958 | 442/18723 | 4.29e-12 | 1.92e-10 | 259 |
| GO:00183942 | Liver | HCC | peptidyl-lysine acetylation | 116/7958 | 169/18723 | 5.11e-12 | 2.23e-10 | 116 |
| GO:004593622 | Liver | HCC | negative regulation of phosphate metabolic process | 258/7958 | 441/18723 | 6.00e-12 | 2.60e-10 | 258 |
| GO:000989522 | Liver | HCC | negative regulation of catabolic process | 196/7958 | 320/18723 | 7.98e-12 | 3.35e-10 | 196 |
| GO:003133022 | Liver | HCC | negative regulation of cellular catabolic process | 164/7958 | 262/18723 | 3.52e-11 | 1.35e-09 | 164 |
| GO:004232622 | Liver | HCC | negative regulation of phosphorylation | 227/7958 | 385/18723 | 3.98e-11 | 1.52e-09 | 227 |
| GO:005134822 | Liver | HCC | negative regulation of transferase activity | 166/7958 | 268/18723 | 8.97e-11 | 3.18e-09 | 166 |
| GO:00064752 | Liver | HCC | internal protein amino acid acetylation | 107/7958 | 160/18723 | 3.77e-10 | 1.23e-08 | 107 |
| GO:00183932 | Liver | HCC | internal peptidyl-lysine acetylation | 105/7958 | 158/18723 | 9.48e-10 | 2.90e-08 | 105 |
| GO:190589712 | Liver | HCC | regulation of response to endoplasmic reticulum stress | 62/7958 | 82/18723 | 1.06e-09 | 3.23e-08 | 62 |
| GO:00165732 | Liver | HCC | histone acetylation | 101/7958 | 152/18723 | 1.99e-09 | 5.63e-08 | 101 |
| GO:000734611 | Liver | HCC | regulation of mitotic cell cycle | 255/7958 | 457/18723 | 4.96e-09 | 1.30e-07 | 255 |
| GO:003367322 | Liver | HCC | negative regulation of kinase activity | 144/7958 | 237/18723 | 9.76e-09 | 2.45e-07 | 144 |
| GO:000193322 | Liver | HCC | negative regulation of protein phosphorylation | 196/7958 | 342/18723 | 1.95e-08 | 4.63e-07 | 196 |
| GO:00439671 | Liver | HCC | histone H4 acetylation | 50/7958 | 67/18723 | 9.14e-08 | 1.82e-06 | 50 |
| GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
| 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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