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Gene: YOD1 |
Gene summary for YOD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | YOD1 | Gene ID | 55432 |
| Gene name | YOD1 deubiquitinase | |
| Gene Alias | DUBA8 | |
| Cytomap | 1q32.1 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q5VVQ6 |
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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 |
| 55432 | YOD1 | P76T-E | Human | Esophagus | ESCC | 6.21e-09 | 5.39e-02 | 0.1207 |
| 55432 | YOD1 | P79T-E | Human | Esophagus | ESCC | 1.54e-06 | 1.14e-02 | 0.1154 |
| 55432 | YOD1 | P80T-E | Human | Esophagus | ESCC | 4.65e-11 | 5.68e-01 | 0.155 |
| 55432 | YOD1 | P82T-E | Human | Esophagus | ESCC | 9.67e-03 | 2.28e-01 | 0.1072 |
| 55432 | YOD1 | P83T-E | Human | Esophagus | ESCC | 1.11e-07 | 2.86e-01 | 0.1738 |
| 55432 | YOD1 | P107T-E | Human | Esophagus | ESCC | 1.15e-07 | 2.38e-01 | 0.171 |
| 55432 | YOD1 | P127T-E | Human | Esophagus | ESCC | 2.31e-24 | 4.76e-01 | 0.0826 |
| 55432 | YOD1 | P128T-E | Human | Esophagus | ESCC | 1.49e-13 | 6.73e-01 | 0.1241 |
| 55432 | YOD1 | P130T-E | Human | Esophagus | ESCC | 2.81e-16 | 4.88e-01 | 0.1676 |
| 55432 | YOD1 | HCC1_Meng | Human | Liver | HCC | 5.68e-09 | -8.86e-03 | 0.0246 |
| 55432 | YOD1 | HCC2_Meng | Human | Liver | HCC | 4.94e-11 | 1.30e-01 | 0.0107 |
| 55432 | YOD1 | HCC1 | Human | Liver | HCC | 4.60e-02 | 2.05e+00 | 0.5336 |
| 55432 | YOD1 | HCC2 | Human | Liver | HCC | 5.09e-06 | 2.70e+00 | 0.5341 |
| 55432 | YOD1 | S016 | Human | Liver | HCC | 2.08e-02 | 1.34e-01 | 0.2243 |
| 55432 | YOD1 | S028 | Human | Liver | HCC | 6.23e-06 | 2.42e-01 | 0.2503 |
| 55432 | YOD1 | S029 | Human | Liver | HCC | 7.14e-06 | 2.80e-01 | 0.2581 |
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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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:0010498111 | Esophagus | ESCC | proteasomal protein catabolic process | 369/8552 | 490/18723 | 1.13e-41 | 1.80e-38 | 369 |
| GO:0043161111 | Esophagus | ESCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 312/8552 | 412/18723 | 3.53e-36 | 4.48e-33 | 312 |
| GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
| GO:003238618 | Esophagus | ESCC | regulation of intracellular transport | 243/8552 | 337/18723 | 3.20e-23 | 7.25e-21 | 243 |
| GO:0034976111 | Esophagus | ESCC | response to endoplasmic reticulum stress | 192/8552 | 256/18723 | 7.15e-22 | 1.30e-19 | 192 |
| GO:0033157110 | Esophagus | ESCC | regulation of intracellular protein transport | 169/8552 | 229/18723 | 3.31e-18 | 3.23e-16 | 169 |
| GO:0035966111 | Esophagus | ESCC | response to topologically incorrect protein | 125/8552 | 159/18723 | 1.44e-17 | 1.27e-15 | 125 |
| GO:0006986111 | Esophagus | ESCC | response to unfolded protein | 107/8552 | 137/18723 | 7.01e-15 | 3.87e-13 | 107 |
| GO:0035967111 | Esophagus | ESCC | cellular response to topologically incorrect protein | 90/8552 | 116/18723 | 1.94e-12 | 8.11e-11 | 90 |
| GO:003650315 | Esophagus | ESCC | ERAD pathway | 82/8552 | 107/18723 | 5.80e-11 | 1.84e-09 | 82 |
| GO:0034620111 | Esophagus | ESCC | cellular response to unfolded protein | 74/8552 | 96/18723 | 3.10e-10 | 8.66e-09 | 74 |
| GO:003043314 | Esophagus | ESCC | ubiquitin-dependent ERAD pathway | 66/8552 | 85/18723 | 1.64e-09 | 3.78e-08 | 66 |
| GO:003096818 | Esophagus | ESCC | endoplasmic reticulum unfolded protein response | 59/8552 | 74/18723 | 1.90e-09 | 4.36e-08 | 59 |
| GO:003252714 | Esophagus | ESCC | protein exit from endoplasmic reticulum | 37/8552 | 48/18723 | 8.99e-06 | 8.65e-05 | 37 |
| GO:19038289 | Esophagus | ESCC | negative regulation of cellular protein localization | 76/8552 | 117/18723 | 1.97e-05 | 1.72e-04 | 76 |
| GO:007064612 | Esophagus | ESCC | protein modification by small protein removal | 95/8552 | 157/18723 | 1.25e-04 | 8.56e-04 | 95 |
| GO:003097014 | Esophagus | ESCC | retrograde protein transport, ER to cytosol | 23/8552 | 29/18723 | 2.25e-04 | 1.40e-03 | 23 |
| GO:190351314 | Esophagus | ESCC | endoplasmic reticulum to cytosol transport | 23/8552 | 29/18723 | 2.25e-04 | 1.40e-03 | 23 |
| GO:00512244 | Esophagus | ESCC | negative regulation of protein transport | 74/8552 | 127/18723 | 2.86e-03 | 1.21e-02 | 74 |
| GO:19049505 | Esophagus | ESCC | negative regulation of establishment of protein localization | 76/8552 | 131/18723 | 2.96e-03 | 1.24e-02 | 76 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04141211 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
| hsa04141310 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
| hsa0414122 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
| hsa0414132 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
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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 |
| YOD1 | SNV | Missense_Mutation | c.551N>T | p.Arg184Leu | p.R184L | Q5VVQ6 | protein_coding | tolerated(0.06) | benign(0.206) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| YOD1 | SNV | Missense_Mutation | novel | c.949A>G | p.Thr317Ala | p.T317A | Q5VVQ6 | protein_coding | tolerated(0.14) | benign(0.006) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| YOD1 | SNV | Missense_Mutation | rs772683929 | c.550C>T | p.Arg184Cys | p.R184C | Q5VVQ6 | protein_coding | deleterious(0.01) | possibly_damaging(0.659) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| YOD1 | SNV | Missense_Mutation | rs772977018 | c.497N>G | p.Tyr166Cys | p.Y166C | Q5VVQ6 | protein_coding | tolerated(0.17) | probably_damaging(0.911) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| YOD1 | SNV | Missense_Mutation | c.229G>A | p.Ala77Thr | p.A77T | Q5VVQ6 | protein_coding | tolerated(0.26) | benign(0.297) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| YOD1 | SNV | Missense_Mutation | novel | c.778C>A | p.Leu260Met | p.L260M | Q5VVQ6 | protein_coding | deleterious(0.01) | probably_damaging(0.955) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| YOD1 | SNV | Missense_Mutation | rs749496673 | c.959N>A | p.Cys320Tyr | p.C320Y | Q5VVQ6 | protein_coding | deleterious(0) | benign(0.007) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| YOD1 | SNV | Missense_Mutation | c.551N>A | p.Arg184His | p.R184H | Q5VVQ6 | protein_coding | tolerated(0.45) | benign(0.005) | TCGA-A5-A2K3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD | |
| YOD1 | SNV | Missense_Mutation | novel | c.392N>A | p.Pro131His | p.P131H | Q5VVQ6 | protein_coding | deleterious(0.02) | benign(0.425) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| YOD1 | SNV | Missense_Mutation | novel | c.505N>A | p.Val169Ile | p.V169I | Q5VVQ6 | protein_coding | tolerated(0.13) | benign(0.348) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | 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 |
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