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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 | LZE4T | Human | Esophagus | ESCC | 4.95e-07 | 1.43e-01 | 0.0811 |
| 55432 | YOD1 | LZE7T | Human | Esophagus | ESCC | 1.23e-02 | 1.06e-01 | 0.0667 |
| 55432 | YOD1 | LZE22T | Human | Esophagus | ESCC | 2.17e-02 | 3.26e-01 | 0.068 |
| 55432 | YOD1 | LZE24T | Human | Esophagus | ESCC | 1.53e-05 | 3.61e-01 | 0.0596 |
| 55432 | YOD1 | P2T-E | Human | Esophagus | ESCC | 7.00e-16 | 7.95e-02 | 0.1177 |
| 55432 | YOD1 | P4T-E | Human | Esophagus | ESCC | 7.47e-05 | 1.96e-01 | 0.1323 |
| 55432 | YOD1 | P5T-E | Human | Esophagus | ESCC | 3.79e-13 | 2.95e-01 | 0.1327 |
| 55432 | YOD1 | P8T-E | Human | Esophagus | ESCC | 1.44e-05 | 1.67e-01 | 0.0889 |
| 55432 | YOD1 | P9T-E | Human | Esophagus | ESCC | 6.05e-04 | 2.78e-01 | 0.1131 |
| 55432 | YOD1 | P10T-E | Human | Esophagus | ESCC | 5.45e-06 | 6.68e-02 | 0.116 |
| 55432 | YOD1 | P12T-E | Human | Esophagus | ESCC | 9.25e-12 | 2.08e-02 | 0.1122 |
| 55432 | YOD1 | P15T-E | Human | Esophagus | ESCC | 4.20e-06 | 2.10e-01 | 0.1149 |
| 55432 | YOD1 | P17T-E | Human | Esophagus | ESCC | 1.25e-03 | 6.80e-02 | 0.1278 |
| 55432 | YOD1 | P20T-E | Human | Esophagus | ESCC | 9.67e-06 | 7.58e-02 | 0.1124 |
| 55432 | YOD1 | P21T-E | Human | Esophagus | ESCC | 2.26e-14 | 8.62e-02 | 0.1617 |
| 55432 | YOD1 | P22T-E | Human | Esophagus | ESCC | 2.39e-09 | 8.81e-02 | 0.1236 |
| 55432 | YOD1 | P23T-E | Human | Esophagus | ESCC | 2.25e-12 | 2.54e-01 | 0.108 |
| 55432 | YOD1 | P24T-E | Human | Esophagus | ESCC | 1.62e-04 | 2.70e-03 | 0.1287 |
| 55432 | YOD1 | P26T-E | Human | Esophagus | ESCC | 2.14e-18 | 2.13e-01 | 0.1276 |
| 55432 | YOD1 | P27T-E | Human | Esophagus | ESCC | 1.82e-06 | 6.69e-02 | 0.1055 |
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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:19035131 | Liver | HCC | endoplasmic reticulum to cytosol transport | 24/7958 | 29/18723 | 1.04e-05 | 1.20e-04 | 24 |
| GO:190382811 | Liver | HCC | negative regulation of cellular protein localization | 71/7958 | 117/18723 | 5.44e-05 | 5.12e-04 | 71 |
| 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:00323871 | Liver | HCC | negative regulation of intracellular transport | 37/7958 | 58/18723 | 8.64e-04 | 5.13e-03 | 37 |
| GO:00708612 | Liver | HCC | regulation of protein exit from endoplasmic reticulum | 20/7958 | 27/18723 | 8.85e-04 | 5.23e-03 | 20 |
| GO:00705361 | Liver | HCC | protein K63-linked deubiquitination | 24/7958 | 35/18723 | 1.64e-03 | 8.61e-03 | 24 |
| GO:19049501 | Liver | HCC | negative regulation of establishment of protein localization | 72/7958 | 131/18723 | 2.65e-03 | 1.27e-02 | 72 |
| GO:00708621 | Liver | HCC | negative regulation of protein exit from endoplasmic reticulum | 9/7958 | 10/18723 | 2.79e-03 | 1.31e-02 | 9 |
| GO:00903171 | Liver | HCC | negative regulation of intracellular protein transport | 27/7958 | 42/18723 | 3.60e-03 | 1.60e-02 | 27 |
| GO:00512241 | Liver | HCC | negative regulation of protein transport | 69/7958 | 127/18723 | 4.67e-03 | 2.01e-02 | 69 |
| GO:00711081 | Liver | HCC | protein K48-linked deubiquitination | 23/7958 | 35/18723 | 4.72e-03 | 2.02e-02 | 23 |
| GO:19041521 | Liver | HCC | regulation of retrograde protein transport, ER to cytosol | 11/7958 | 14/18723 | 6.81e-03 | 2.73e-02 | 11 |
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| 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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