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Gene: USP54 |
Gene summary for USP54 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | USP54 | Gene ID | 159195 |
| Gene name | ubiquitin specific peptidase 54 | |
| Gene Alias | C10orf29 | |
| Cytomap | 10q22.2 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | B7Z7X1 |
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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 |
| 159195 | USP54 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.42e-03 | -3.15e-01 | 0.0155 |
| 159195 | USP54 | HTA11_7862_2000001011 | Human | Colorectum | AD | 1.37e-03 | -4.16e-01 | -0.0179 |
| 159195 | USP54 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 8.74e-10 | -3.43e-01 | 0.294 |
| 159195 | USP54 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.70e-09 | -4.34e-01 | 0.3005 |
| 159195 | USP54 | A002-C-010 | Human | Colorectum | FAP | 4.04e-02 | 1.69e-01 | 0.242 |
| 159195 | USP54 | A015-C-203 | Human | Colorectum | FAP | 1.34e-25 | -1.68e-01 | -0.1294 |
| 159195 | USP54 | A015-C-204 | Human | Colorectum | FAP | 1.15e-02 | -1.14e-01 | -0.0228 |
| 159195 | USP54 | A014-C-040 | Human | Colorectum | FAP | 1.14e-02 | -1.38e-01 | -0.1184 |
| 159195 | USP54 | A002-C-201 | Human | Colorectum | FAP | 2.22e-11 | -5.18e-02 | 0.0324 |
| 159195 | USP54 | A001-C-119 | Human | Colorectum | FAP | 1.74e-04 | 5.18e-02 | -0.1557 |
| 159195 | USP54 | A001-C-108 | Human | Colorectum | FAP | 9.11e-15 | -1.19e-01 | -0.0272 |
| 159195 | USP54 | A002-C-021 | Human | Colorectum | FAP | 4.23e-02 | 3.10e-01 | 0.1171 |
| 159195 | USP54 | A002-C-205 | Human | Colorectum | FAP | 8.28e-19 | -9.34e-02 | -0.1236 |
| 159195 | USP54 | A015-C-006 | Human | Colorectum | FAP | 4.18e-16 | -3.45e-01 | -0.0994 |
| 159195 | USP54 | A015-C-106 | Human | Colorectum | FAP | 3.86e-08 | -1.30e-01 | -0.0511 |
| 159195 | USP54 | A002-C-114 | Human | Colorectum | FAP | 2.69e-16 | -5.99e-02 | -0.1561 |
| 159195 | USP54 | A015-C-104 | Human | Colorectum | FAP | 5.98e-27 | -1.58e-01 | -0.1899 |
| 159195 | USP54 | A001-C-014 | Human | Colorectum | FAP | 4.07e-10 | -1.40e-01 | 0.0135 |
| 159195 | USP54 | A002-C-016 | Human | Colorectum | FAP | 1.92e-20 | -1.05e-01 | 0.0521 |
| 159195 | USP54 | A015-C-002 | Human | Colorectum | FAP | 9.95e-11 | -2.22e-01 | -0.0763 |
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid 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:00706461 | Liver | HCC | protein modification by small protein removal | 91/7958 | 157/18723 | 6.50e-05 | 5.92e-04 | 91 |
| GO:00165791 | Liver | HCC | protein deubiquitination | 78/7958 | 139/18723 | 8.13e-04 | 4.87e-03 | 78 |
| GO:00706465 | Thyroid | PTC | protein modification by small protein removal | 71/5968 | 157/18723 | 3.03e-04 | 2.12e-03 | 71 |
| GO:00165794 | Thyroid | PTC | protein deubiquitination | 59/5968 | 139/18723 | 5.50e-03 | 2.50e-02 | 59 |
| GO:007064613 | Thyroid | ATC | protein modification by small protein removal | 71/6293 | 157/18723 | 1.59e-03 | 7.99e-03 | 71 |
| Page: 1 |
| 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 |
| USP54 | SNV | Missense_Mutation | novel | c.2081N>T | p.Ser694Leu | p.S694L | Q70EL1 | protein_coding | tolerated(0.11) | benign(0) | TCGA-A8-A06Q-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| USP54 | SNV | Missense_Mutation | rs369153358 | c.1414G>A | p.Asp472Asn | p.D472N | Q70EL1 | protein_coding | deleterious(0.03) | benign(0.2) | TCGA-A8-A09G-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| USP54 | SNV | Missense_Mutation | c.4012N>C | p.Gly1338Arg | p.G1338R | Q70EL1 | protein_coding | tolerated(0.16) | benign(0.028) | TCGA-B6-A0RN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| USP54 | SNV | Missense_Mutation | c.4235N>C | p.Leu1412Ser | p.L1412S | Q70EL1 | protein_coding | deleterious(0) | benign(0) | TCGA-BH-A0BL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | |
| USP54 | SNV | Missense_Mutation | novel | c.663T>G | p.Asp221Glu | p.D221E | Q70EL1 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD |
| USP54 | SNV | Missense_Mutation | rs368763438 | c.2590C>T | p.Arg864Cys | p.R864C | Q70EL1 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E9-A249-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| USP54 | SNV | Missense_Mutation | novel | c.2441N>A | p.Gly814Glu | p.G814E | Q70EL1 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-OL-A97C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| USP54 | SNV | Missense_Mutation | novel | c.2774N>T | p.Ser925Leu | p.S925L | Q70EL1 | protein_coding | tolerated_low_confidence(0.54) | benign(0.015) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| USP54 | insertion | Frame_Shift_Ins | novel | c.2254_2255insTCAGACAGGTCAGATGCAAAGGACAA | p.Ala752ValfsTer23 | p.A752Vfs*23 | Q70EL1 | protein_coding | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | SD | |||
| USP54 | insertion | Nonsense_Mutation | novel | c.2247_2248insTTCAAAATAGTTCAGCCAAGCTGAAGTATCTACCTTAAATAGGCCAT | p.Arg750PhefsTer8 | p.R750Ffs*8 | Q70EL1 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
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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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