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Gene: TDP2 |
Gene summary for TDP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TDP2 | Gene ID | 51567 |
| Gene name | tyrosyl-DNA phosphodiesterase 2 | |
| Gene Alias | AD022 | |
| Cytomap | 6p22.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | O95551 |
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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 |
| 51567 | TDP2 | P128T-E | Human | Esophagus | ESCC | 3.36e-43 | 1.19e+00 | 0.1241 |
| 51567 | TDP2 | P130T-E | Human | Esophagus | ESCC | 1.42e-47 | 1.08e+00 | 0.1676 |
| 51567 | TDP2 | HCC1_Meng | Human | Liver | HCC | 1.63e-65 | 2.28e-01 | 0.0246 |
| 51567 | TDP2 | HCC2_Meng | Human | Liver | HCC | 8.45e-18 | 6.92e-02 | 0.0107 |
| 51567 | TDP2 | HCC2 | Human | Liver | HCC | 1.83e-10 | 2.76e+00 | 0.5341 |
| 51567 | TDP2 | Pt13.a | Human | Liver | HCC | 1.68e-02 | 2.27e-01 | 0.021 |
| 51567 | TDP2 | Pt13.b | Human | Liver | HCC | 1.01e-18 | 2.60e-01 | 0.0251 |
| 51567 | TDP2 | S014 | Human | Liver | HCC | 1.44e-08 | 3.32e-01 | 0.2254 |
| 51567 | TDP2 | S015 | Human | Liver | HCC | 3.18e-07 | 4.51e-01 | 0.2375 |
| 51567 | TDP2 | S016 | Human | Liver | HCC | 3.46e-09 | 3.74e-01 | 0.2243 |
| 51567 | TDP2 | S027 | Human | Liver | HCC | 5.03e-08 | 4.24e-01 | 0.2446 |
| 51567 | TDP2 | S028 | Human | Liver | HCC | 2.02e-16 | 6.70e-01 | 0.2503 |
| 51567 | TDP2 | S029 | Human | Liver | HCC | 3.09e-10 | 6.59e-01 | 0.2581 |
| 51567 | TDP2 | C04 | Human | Oral cavity | OSCC | 6.90e-18 | 8.05e-01 | 0.2633 |
| 51567 | TDP2 | C21 | Human | Oral cavity | OSCC | 6.58e-41 | 1.08e+00 | 0.2678 |
| 51567 | TDP2 | C30 | Human | Oral cavity | OSCC | 1.65e-21 | 9.39e-01 | 0.3055 |
| 51567 | TDP2 | C38 | Human | Oral cavity | OSCC | 5.50e-05 | 5.40e-01 | 0.172 |
| 51567 | TDP2 | C43 | Human | Oral cavity | OSCC | 7.57e-12 | 3.29e-01 | 0.1704 |
| 51567 | TDP2 | C46 | Human | Oral cavity | OSCC | 2.89e-12 | 3.60e-01 | 0.1673 |
| 51567 | TDP2 | C51 | Human | Oral cavity | OSCC | 1.70e-12 | 5.24e-01 | 0.2674 |
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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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
| GO:00063024 | Esophagus | ESCC | double-strand break repair | 152/8552 | 251/18723 | 1.33e-06 | 1.62e-05 | 152 |
| GO:0090305 | Liver | HCC | nucleic acid phosphodiester bond hydrolysis | 152/7958 | 261/18723 | 1.90e-07 | 3.46e-06 | 152 |
| GO:00063021 | Liver | HCC | double-strand break repair | 131/7958 | 251/18723 | 1.17e-03 | 6.54e-03 | 131 |
| GO:00903052 | Oral cavity | OSCC | nucleic acid phosphodiester bond hydrolysis | 142/7305 | 261/18723 | 2.90e-07 | 4.43e-06 | 142 |
| GO:00063023 | Oral cavity | OSCC | double-strand break repair | 132/7305 | 251/18723 | 7.93e-06 | 8.52e-05 | 132 |
| GO:00903051 | Oral cavity | LP | nucleic acid phosphodiester bond hydrolysis | 92/4623 | 261/18723 | 8.07e-05 | 1.04e-03 | 92 |
| GO:000630211 | Oral cavity | LP | double-strand break repair | 80/4623 | 251/18723 | 5.81e-03 | 3.46e-02 | 80 |
| GO:00903054 | Skin | cSCC | nucleic acid phosphodiester bond hydrolysis | 97/4864 | 261/18723 | 4.08e-05 | 4.34e-04 | 97 |
| GO:00063025 | Skin | cSCC | double-strand break repair | 89/4864 | 251/18723 | 5.23e-04 | 3.92e-03 | 89 |
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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 |
| TDP2 | SNV | Missense_Mutation | c.655N>C | p.Glu219Gln | p.E219Q | O95551 | protein_coding | tolerated(0.05) | benign(0.439) | TCGA-C5-A8YQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| TDP2 | SNV | Missense_Mutation | c.272A>C | p.Glu91Ala | p.E91A | O95551 | protein_coding | tolerated(0.55) | benign(0.007) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| TDP2 | SNV | Missense_Mutation | c.710N>A | p.Arg237Gln | p.R237Q | O95551 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TDP2 | SNV | Missense_Mutation | novel | c.995G>A | p.Arg332Gln | p.R332Q | O95551 | protein_coding | tolerated(1) | benign(0.007) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TDP2 | SNV | Missense_Mutation | novel | c.491G>T | p.Arg164Ile | p.R164I | O95551 | protein_coding | deleterious(0.04) | benign(0.392) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TDP2 | SNV | Missense_Mutation | c.85T>A | p.Cys29Ser | p.C29S | O95551 | protein_coding | deleterious(0.02) | benign(0.197) | TCGA-G5-6641-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| TDP2 | deletion | Frame_Shift_Del | c.71delN | p.Lys24SerfsTer35 | p.K24Sfs*35 | O95551 | protein_coding | TCGA-AA-A01P-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |||
| TDP2 | SNV | Missense_Mutation | c.710N>T | p.Arg237Leu | p.R237L | O95551 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TDP2 | SNV | Missense_Mutation | c.796A>G | p.Arg266Gly | p.R266G | O95551 | protein_coding | deleterious(0) | probably_damaging(0.925) | TCGA-AP-A054-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD | |
| TDP2 | SNV | Missense_Mutation | rs745911675 | c.940N>T | p.Arg314Cys | p.R314C | O95551 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | 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 |
| 51567 | TDP2 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | 9,10-PHENANTHRENEQUINONE | 9,10-PHENANTHRENEQUINONE | ||
| 51567 | TDP2 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | GNF-PF-4418 | CHEMBL604321 | ||
| 51567 | TDP2 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | (-)-DICENTRINE | CHEMBL478754 |
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