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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:190179911 | Endometrium | EEC | negative regulation of proteasomal protein catabolic process | 16/2168 | 49/18723 | 7.80e-05 | 1.13e-03 | 16 |
| GO:190589717 | Endometrium | EEC | regulation of response to endoplasmic reticulum stress | 22/2168 | 82/18723 | 1.14e-04 | 1.54e-03 | 22 |
| GO:190357316 | Endometrium | EEC | negative regulation of response to endoplasmic reticulum stress | 14/2168 | 44/18723 | 2.94e-04 | 3.30e-03 | 14 |
| GO:003650312 | Endometrium | EEC | ERAD pathway | 24/2168 | 107/18723 | 1.03e-03 | 9.07e-03 | 24 |
| GO:00182057 | Esophagus | HGIN | peptidyl-lysine modification | 88/2587 | 376/18723 | 2.99e-07 | 1.39e-05 | 88 |
| GO:000734610 | Esophagus | HGIN | regulation of mitotic cell cycle | 98/2587 | 457/18723 | 4.39e-06 | 1.42e-04 | 98 |
| GO:00165708 | Esophagus | HGIN | histone modification | 92/2587 | 463/18723 | 1.70e-04 | 3.30e-03 | 92 |
| GO:00165747 | Esophagus | HGIN | histone ubiquitination | 16/2587 | 47/18723 | 3.61e-04 | 5.68e-03 | 16 |
| GO:00064735 | Esophagus | HGIN | protein acetylation | 45/2587 | 201/18723 | 6.17e-04 | 8.58e-03 | 45 |
| GO:00183945 | Esophagus | HGIN | peptidyl-lysine acetylation | 39/2587 | 169/18723 | 7.46e-04 | 9.90e-03 | 39 |
| GO:00435435 | Esophagus | HGIN | protein acylation | 51/2587 | 243/18723 | 1.33e-03 | 1.57e-02 | 51 |
| GO:00439675 | Esophagus | HGIN | histone H4 acetylation | 19/2587 | 67/18723 | 1.39e-03 | 1.63e-02 | 19 |
| GO:00064755 | Esophagus | HGIN | internal protein amino acid acetylation | 36/2587 | 160/18723 | 1.87e-03 | 2.01e-02 | 36 |
| GO:00183935 | Esophagus | HGIN | internal peptidyl-lysine acetylation | 35/2587 | 158/18723 | 2.82e-03 | 2.75e-02 | 35 |
| GO:004593110 | Esophagus | HGIN | positive regulation of mitotic cell cycle | 28/2587 | 121/18723 | 3.72e-03 | 3.39e-02 | 28 |
| GO:00706463 | Esophagus | HGIN | protein modification by small protein removal | 34/2587 | 157/18723 | 4.68e-03 | 4.02e-02 | 34 |
| GO:0097193111 | Esophagus | ESCC | intrinsic apoptotic signaling pathway | 222/8552 | 288/18723 | 5.87e-28 | 2.02e-25 | 222 |
| GO:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
| GO:0031647111 | Esophagus | ESCC | regulation of protein stability | 223/8552 | 298/18723 | 5.76e-25 | 1.52e-22 | 223 |
| GO:001820514 | Esophagus | ESCC | peptidyl-lysine modification | 259/8552 | 376/18723 | 3.90e-20 | 5.26e-18 | 259 |
| 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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