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Gene: USP38 |
Gene summary for USP38 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | USP38 | Gene ID | 84640 |
| Gene name | ubiquitin specific peptidase 38 | |
| Gene Alias | HP43.8KD | |
| Cytomap | 4q31.21 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q8NB14 |
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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 |
| 84640 | USP38 | P21T-E | Human | Esophagus | ESCC | 5.24e-11 | -1.38e-02 | 0.1617 |
| 84640 | USP38 | P22T-E | Human | Esophagus | ESCC | 1.74e-11 | 2.34e-02 | 0.1236 |
| 84640 | USP38 | P23T-E | Human | Esophagus | ESCC | 6.26e-06 | -2.35e-02 | 0.108 |
| 84640 | USP38 | P24T-E | Human | Esophagus | ESCC | 1.04e-11 | -2.20e-02 | 0.1287 |
| 84640 | USP38 | P26T-E | Human | Esophagus | ESCC | 3.20e-15 | 1.23e-01 | 0.1276 |
| 84640 | USP38 | P27T-E | Human | Esophagus | ESCC | 4.83e-16 | 1.47e-02 | 0.1055 |
| 84640 | USP38 | P28T-E | Human | Esophagus | ESCC | 5.85e-08 | 1.67e-01 | 0.1149 |
| 84640 | USP38 | P30T-E | Human | Esophagus | ESCC | 7.70e-06 | 7.94e-03 | 0.137 |
| 84640 | USP38 | P31T-E | Human | Esophagus | ESCC | 3.80e-08 | -5.34e-02 | 0.1251 |
| 84640 | USP38 | P32T-E | Human | Esophagus | ESCC | 2.71e-08 | 5.22e-03 | 0.1666 |
| 84640 | USP38 | P36T-E | Human | Esophagus | ESCC | 2.32e-02 | 2.54e-01 | 0.1187 |
| 84640 | USP38 | P37T-E | Human | Esophagus | ESCC | 2.47e-08 | -1.02e-02 | 0.1371 |
| 84640 | USP38 | P39T-E | Human | Esophagus | ESCC | 5.87e-08 | -1.05e-01 | 0.0894 |
| 84640 | USP38 | P40T-E | Human | Esophagus | ESCC | 7.24e-07 | -1.18e-02 | 0.109 |
| 84640 | USP38 | P42T-E | Human | Esophagus | ESCC | 2.78e-05 | 1.63e-01 | 0.1175 |
| 84640 | USP38 | P44T-E | Human | Esophagus | ESCC | 1.40e-06 | -7.37e-02 | 0.1096 |
| 84640 | USP38 | P47T-E | Human | Esophagus | ESCC | 1.25e-10 | 5.12e-04 | 0.1067 |
| 84640 | USP38 | P49T-E | Human | Esophagus | ESCC | 1.72e-05 | 5.50e-01 | 0.1768 |
| 84640 | USP38 | P52T-E | Human | Esophagus | ESCC | 2.76e-11 | 2.03e-01 | 0.1555 |
| 84640 | USP38 | P54T-E | Human | Esophagus | ESCC | 9.23e-03 | 6.11e-02 | 0.0975 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias |
| ∗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:007064612 | Esophagus | ESCC | protein modification by small protein removal | 95/8552 | 157/18723 | 1.25e-04 | 8.56e-04 | 95 |
| GO:00165793 | Esophagus | ESCC | protein deubiquitination | 79/8552 | 139/18723 | 5.23e-03 | 1.97e-02 | 79 |
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| 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. |
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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 |
| USP38 | SNV | Missense_Mutation | c.773N>G | p.Thr258Arg | p.T258R | Q8NB14 | protein_coding | deleterious(0) | possibly_damaging(0.586) | TCGA-AO-A0J4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| USP38 | SNV | Missense_Mutation | c.825N>G | p.Ile275Met | p.I275M | Q8NB14 | protein_coding | tolerated(0.07) | probably_damaging(0.973) | TCGA-BH-A0GY-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyotxan | SD | |
| USP38 | SNV | Missense_Mutation | c.115N>C | p.Glu39Gln | p.E39Q | Q8NB14 | protein_coding | tolerated(0.46) | benign(0.001) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR | |
| USP38 | SNV | Missense_Mutation | c.115G>C | p.Glu39Gln | p.E39Q | Q8NB14 | protein_coding | tolerated(0.46) | benign(0.001) | TCGA-C5-A3HL-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| USP38 | SNV | Missense_Mutation | c.286N>G | p.Leu96Val | p.L96V | Q8NB14 | protein_coding | tolerated(0.28) | benign(0.007) | TCGA-DS-A0VN-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| USP38 | SNV | Missense_Mutation | c.236T>C | p.Phe79Ser | p.F79S | Q8NB14 | protein_coding | deleterious(0.01) | possibly_damaging(0.452) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| USP38 | SNV | Missense_Mutation | c.1603A>G | p.Arg535Gly | p.R535G | Q8NB14 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| USP38 | SNV | Missense_Mutation | c.2855C>T | p.Thr952Ile | p.T952I | Q8NB14 | protein_coding | tolerated(0.18) | benign(0.042) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| USP38 | SNV | Missense_Mutation | novel | c.326N>C | p.Asn109Thr | p.N109T | Q8NB14 | protein_coding | tolerated(0.65) | benign(0.031) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| USP38 | SNV | Missense_Mutation | c.2171N>G | p.Tyr724Cys | p.Y724C | Q8NB14 | protein_coding | deleterious(0) | possibly_damaging(0.81) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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 |
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