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Gene: USP12 |
Gene summary for USP12 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | USP12 | Gene ID | 219333 |
| Gene name | ubiquitin specific peptidase 12 | |
| Gene Alias | UBH1 | |
| Cytomap | 13q12.13 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | O75317 |
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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 |
| 219333 | USP12 | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.28e-14 | -5.44e-01 | 0.0155 |
| 219333 | USP12 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.28e-04 | -3.77e-01 | -0.1808 |
| 219333 | USP12 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.48e-02 | -4.27e-01 | -0.1207 |
| 219333 | USP12 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.38e-07 | -4.01e-01 | -0.1464 |
| 219333 | USP12 | HTA11_866_2000001011 | Human | Colorectum | AD | 6.47e-07 | -3.92e-01 | -0.1001 |
| 219333 | USP12 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.85e-02 | -4.84e-01 | -0.0842 |
| 219333 | USP12 | HTA11_866_3004761011 | Human | Colorectum | AD | 5.73e-12 | -5.33e-01 | 0.096 |
| 219333 | USP12 | HTA11_10711_2000001011 | Human | Colorectum | AD | 9.33e-04 | -4.68e-01 | 0.0338 |
| 219333 | USP12 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.12e-12 | -4.82e-01 | 0.0674 |
| 219333 | USP12 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.72e-08 | -4.06e-01 | 0.294 |
| 219333 | USP12 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.41e-18 | -5.68e-01 | 0.3005 |
| 219333 | USP12 | A015-C-203 | Human | Colorectum | FAP | 1.64e-21 | -3.57e-01 | -0.1294 |
| 219333 | USP12 | A015-C-204 | Human | Colorectum | FAP | 3.52e-05 | -2.58e-01 | -0.0228 |
| 219333 | USP12 | A014-C-040 | Human | Colorectum | FAP | 6.67e-03 | -2.41e-01 | -0.1184 |
| 219333 | USP12 | A002-C-201 | Human | Colorectum | FAP | 6.99e-13 | -3.26e-01 | 0.0324 |
| 219333 | USP12 | A002-C-203 | Human | Colorectum | FAP | 3.55e-02 | -2.22e-01 | 0.2786 |
| 219333 | USP12 | A001-C-119 | Human | Colorectum | FAP | 7.13e-05 | -3.50e-01 | -0.1557 |
| 219333 | USP12 | A001-C-108 | Human | Colorectum | FAP | 1.77e-09 | -2.54e-01 | -0.0272 |
| 219333 | USP12 | A002-C-205 | Human | Colorectum | FAP | 6.42e-18 | -3.03e-01 | -0.1236 |
| 219333 | USP12 | A015-C-005 | Human | Colorectum | FAP | 2.36e-02 | -1.90e-01 | -0.0336 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
| GO:00059969 | Esophagus | ESCC | monosaccharide metabolic process | 159/8552 | 257/18723 | 1.11e-07 | 1.81e-06 | 159 |
| GO:00193189 | Esophagus | ESCC | hexose metabolic process | 147/8552 | 237/18723 | 2.63e-07 | 3.94e-06 | 147 |
| GO:003367420 | Esophagus | ESCC | positive regulation of kinase activity | 260/8552 | 467/18723 | 7.26e-06 | 7.22e-05 | 260 |
| GO:00060069 | Esophagus | ESCC | glucose metabolic process | 119/8552 | 196/18723 | 1.51e-05 | 1.36e-04 | 119 |
| GO:007064612 | Esophagus | ESCC | protein modification by small protein removal | 95/8552 | 157/18723 | 1.25e-04 | 8.56e-04 | 95 |
| GO:00442626 | Esophagus | ESCC | cellular carbohydrate metabolic process | 160/8552 | 283/18723 | 1.43e-04 | 9.66e-04 | 160 |
| GO:00620129 | Esophagus | ESCC | regulation of small molecule metabolic process | 184/8552 | 334/18723 | 3.11e-04 | 1.85e-03 | 184 |
| GO:00109065 | Esophagus | ESCC | regulation of glucose metabolic process | 71/8552 | 119/18723 | 1.46e-03 | 6.92e-03 | 71 |
| GO:00061096 | Esophagus | ESCC | regulation of carbohydrate metabolic process | 101/8552 | 178/18723 | 1.89e-03 | 8.52e-03 | 101 |
| GO:00106755 | Esophagus | ESCC | regulation of cellular carbohydrate metabolic process | 83/8552 | 146/18723 | 4.24e-03 | 1.69e-02 | 83 |
| GO:00165793 | Esophagus | ESCC | protein deubiquitination | 79/8552 | 139/18723 | 5.23e-03 | 1.97e-02 | 79 |
| GO:000599621 | Liver | HCC | monosaccharide metabolic process | 167/7958 | 257/18723 | 2.31e-13 | 1.25e-11 | 167 |
| GO:001931821 | Liver | HCC | hexose metabolic process | 155/7958 | 237/18723 | 7.63e-13 | 3.90e-11 | 155 |
| GO:000600621 | Liver | HCC | glucose metabolic process | 128/7958 | 196/18723 | 8.60e-11 | 3.06e-09 | 128 |
| GO:006201222 | Liver | HCC | regulation of small molecule metabolic process | 190/7958 | 334/18723 | 6.77e-08 | 1.40e-06 | 190 |
| GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
| GO:000647021 | Liver | HCC | protein dephosphorylation | 162/7958 | 281/18723 | 1.91e-07 | 3.46e-06 | 162 |
| GO:000610921 | Liver | HCC | regulation of carbohydrate metabolic process | 109/7958 | 178/18723 | 3.36e-07 | 5.78e-06 | 109 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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 |
| USP12 | SNV | Missense_Mutation | rs759422176 | c.733N>T | p.Arg245Trp | p.R245W | O75317 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-A7-A13E-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | bevacizumab | PD |
| USP12 | SNV | Missense_Mutation | c.568N>A | p.Glu190Lys | p.E190K | O75317 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| USP12 | SNV | Missense_Mutation | rs760502670 | c.944G>A | p.Arg315Gln | p.R315Q | O75317 | protein_coding | tolerated(0.07) | probably_damaging(0.983) | TCGA-AN-A0XN-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| USP12 | SNV | Missense_Mutation | rs759422176 | c.733N>T | p.Arg245Trp | p.R245W | O75317 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-B6-A0RV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| USP12 | SNV | Missense_Mutation | novel | c.256G>C | p.Asp86His | p.D86H | O75317 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| USP12 | SNV | Missense_Mutation | c.241N>A | p.Leu81Ile | p.L81I | O75317 | protein_coding | deleterious(0.01) | possibly_damaging(0.795) | TCGA-BH-A0B9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| USP12 | SNV | Missense_Mutation | novel | c.689N>G | p.Lys230Arg | p.K230R | O75317 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E9-A3X8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphane | CR |
| USP12 | SNV | Missense_Mutation | c.1000G>A | p.Asp334Asn | p.D334N | O75317 | protein_coding | tolerated(0.06) | possibly_damaging(0.74) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| USP12 | SNV | Missense_Mutation | c.800N>T | p.Gln267Leu | p.Q267L | O75317 | protein_coding | deleterious(0.02) | possibly_damaging(0.506) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| USP12 | SNV | Missense_Mutation | novel | c.88G>A | p.Glu30Lys | p.E30K | O75317 | protein_coding | tolerated(0.19) | benign(0.275) | TCGA-MA-AA3Z-01 | Cervix | cervical & endocervical cancer | Female | <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 |
| Page: 1 |
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