|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: TDP1 |
Gene summary for TDP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TDP1 | Gene ID | 55775 |
| Gene name | tyrosyl-DNA phosphodiesterase 1 | |
| Gene Alias | TDP1 | |
| Cytomap | 14q32.11 | |
| Gene Type | protein-coding | GO ID | GO:0000012 | UniProtAcc | A0A024R6L5 |
Top |
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 |
| 55775 | TDP1 | LZE4T | Human | Esophagus | ESCC | 1.15e-05 | 1.21e-01 | 0.0811 |
| 55775 | TDP1 | LZE7T | Human | Esophagus | ESCC | 2.58e-03 | 1.45e-01 | 0.0667 |
| 55775 | TDP1 | LZE24T | Human | Esophagus | ESCC | 2.23e-09 | 1.88e-01 | 0.0596 |
| 55775 | TDP1 | P1T-E | Human | Esophagus | ESCC | 9.50e-03 | 1.34e-01 | 0.0875 |
| 55775 | TDP1 | P2T-E | Human | Esophagus | ESCC | 2.08e-08 | 2.21e-01 | 0.1177 |
| 55775 | TDP1 | P4T-E | Human | Esophagus | ESCC | 2.17e-11 | 3.20e-01 | 0.1323 |
| 55775 | TDP1 | P5T-E | Human | Esophagus | ESCC | 5.40e-06 | 1.53e-01 | 0.1327 |
| 55775 | TDP1 | P8T-E | Human | Esophagus | ESCC | 1.60e-05 | 1.37e-01 | 0.0889 |
| 55775 | TDP1 | P10T-E | Human | Esophagus | ESCC | 5.23e-12 | 2.33e-01 | 0.116 |
| 55775 | TDP1 | P11T-E | Human | Esophagus | ESCC | 1.32e-04 | 1.76e-01 | 0.1426 |
| 55775 | TDP1 | P12T-E | Human | Esophagus | ESCC | 1.73e-18 | 2.92e-01 | 0.1122 |
| 55775 | TDP1 | P15T-E | Human | Esophagus | ESCC | 2.99e-12 | 3.15e-01 | 0.1149 |
| 55775 | TDP1 | P16T-E | Human | Esophagus | ESCC | 2.22e-09 | 2.11e-01 | 0.1153 |
| 55775 | TDP1 | P17T-E | Human | Esophagus | ESCC | 1.17e-02 | 2.38e-01 | 0.1278 |
| 55775 | TDP1 | P20T-E | Human | Esophagus | ESCC | 8.33e-07 | 1.46e-01 | 0.1124 |
| 55775 | TDP1 | P21T-E | Human | Esophagus | ESCC | 8.00e-11 | 1.80e-01 | 0.1617 |
| 55775 | TDP1 | P22T-E | Human | Esophagus | ESCC | 1.64e-03 | 6.23e-02 | 0.1236 |
| 55775 | TDP1 | P23T-E | Human | Esophagus | ESCC | 8.85e-07 | 1.61e-01 | 0.108 |
| 55775 | TDP1 | P24T-E | Human | Esophagus | ESCC | 1.82e-05 | 1.70e-01 | 0.1287 |
| 55775 | TDP1 | P26T-E | Human | Esophagus | ESCC | 1.17e-08 | 2.00e-01 | 0.1276 |
| Page: 1 2 3 |
| 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. |
Top |
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: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:001603220 | Oral cavity | OSCC | viral process | 274/7305 | 415/18723 | 2.42e-29 | 1.70e-26 | 274 |
| GO:01400145 | Oral cavity | OSCC | mitotic nuclear division | 191/7305 | 287/18723 | 1.99e-21 | 3.70e-19 | 191 |
| GO:00447728 | Oral cavity | OSCC | mitotic cell cycle phase transition | 255/7305 | 424/18723 | 5.29e-19 | 6.98e-17 | 255 |
| GO:001604917 | Oral cavity | OSCC | cell growth | 268/7305 | 482/18723 | 6.55e-14 | 3.51e-12 | 268 |
| GO:004440320 | Oral cavity | OSCC | biological process involved in symbiotic interaction | 173/7305 | 290/18723 | 6.80e-13 | 3.19e-11 | 173 |
| GO:00482852 | Oral cavity | OSCC | organelle fission | 265/7305 | 488/18723 | 3.22e-12 | 1.27e-10 | 265 |
| GO:001908010 | Oral cavity | OSCC | viral gene expression | 69/7305 | 94/18723 | 1.26e-11 | 4.44e-10 | 69 |
| GO:000155816 | Oral cavity | OSCC | regulation of cell growth | 228/7305 | 414/18723 | 1.74e-11 | 6.09e-10 | 228 |
| GO:00002801 | Oral cavity | OSCC | nuclear division | 237/7305 | 439/18723 | 9.62e-11 | 2.90e-09 | 237 |
| GO:000647015 | Oral cavity | OSCC | protein dephosphorylation | 162/7305 | 281/18723 | 1.56e-10 | 4.56e-09 | 162 |
| GO:00063547 | Oral cavity | OSCC | DNA-templated transcription, elongation | 63/7305 | 91/18723 | 4.86e-09 | 1.07e-07 | 63 |
| GO:00163119 | Oral cavity | OSCC | dephosphorylation | 220/7305 | 417/18723 | 6.33e-09 | 1.34e-07 | 220 |
| GO:00063686 | Oral cavity | OSCC | transcription elongation from RNA polymerase II promoter | 48/7305 | 69/18723 | 2.60e-07 | 4.05e-06 | 48 |
| GO:00518176 | Oral cavity | OSCC | modulation of process of other organism involved in symbiotic interaction | 54/7305 | 81/18723 | 4.22e-07 | 6.25e-06 | 54 |
| GO:00459266 | Oral cavity | OSCC | negative regulation of growth | 135/7305 | 249/18723 | 7.29e-07 | 1.03e-05 | 135 |
| GO:00190833 | Oral cavity | OSCC | viral transcription | 36/7305 | 50/18723 | 2.26e-06 | 2.87e-05 | 36 |
| GO:00358218 | Oral cavity | OSCC | modulation of process of other organism | 64/7305 | 106/18723 | 6.70e-06 | 7.36e-05 | 64 |
| GO:00518517 | Oral cavity | OSCC | modulation by host of symbiont process | 40/7305 | 60/18723 | 1.32e-05 | 1.33e-04 | 40 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa034104 | Esophagus | ESCC | Base excision repair | 38/4205 | 44/8465 | 3.59e-07 | 2.62e-06 | 1.34e-06 | 38 |
| hsa0341011 | Esophagus | ESCC | Base excision repair | 38/4205 | 44/8465 | 3.59e-07 | 2.62e-06 | 1.34e-06 | 38 |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| TDP1 | SNV | Missense_Mutation | rs766476915 | c.1459N>T | p.Arg487Cys | p.R487C | Q9NUW8 | protein_coding | deleterious(0.01) | probably_damaging(0.99) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TDP1 | SNV | Missense_Mutation | c.377N>C | p.Arg126Thr | p.R126T | Q9NUW8 | protein_coding | tolerated(0.09) | benign(0) | TCGA-C5-A3HL-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TDP1 | SNV | Missense_Mutation | c.436N>A | p.Glu146Lys | p.E146K | Q9NUW8 | protein_coding | tolerated(0.08) | benign(0.003) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| TDP1 | SNV | Missense_Mutation | rs772139596 | c.1799N>T | p.Thr600Met | p.T600M | Q9NUW8 | protein_coding | deleterious(0.01) | possibly_damaging(0.89) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TDP1 | SNV | Missense_Mutation | c.1571N>T | p.Ala524Val | p.A524V | Q9NUW8 | protein_coding | tolerated(0.13) | benign(0.013) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD | |
| TDP1 | SNV | Missense_Mutation | c.1177C>T | p.Pro393Ser | p.P393S | Q9NUW8 | protein_coding | deleterious(0.03) | probably_damaging(0.998) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TDP1 | SNV | Missense_Mutation | rs765018747 | c.1219N>A | p.Asp407Asn | p.D407N | Q9NUW8 | protein_coding | tolerated(0.06) | benign(0.401) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TDP1 | SNV | Missense_Mutation | novel | c.97C>A | p.Leu33Ile | p.L33I | Q9NUW8 | protein_coding | tolerated_low_confidence(0.15) | benign(0.014) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TDP1 | SNV | Missense_Mutation | novel | c.97N>A | p.Leu33Ile | p.L33I | Q9NUW8 | protein_coding | tolerated_low_confidence(0.15) | benign(0.014) | TCGA-A5-A0GG-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TDP1 | SNV | Missense_Mutation | novel | c.1289C>T | p.Pro430Leu | p.P430L | Q9NUW8 | protein_coding | tolerated(0.79) | benign(0) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 |
Top |
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 |
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | FUMARPROTOCETRARIC ACID | FUMARPROTOCETRARIC ACID | ||
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | TESTOSTERONE | TESTOSTERONE | 19883083 | |
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | ELLIPTECINE | ELLIPTECINE | ||
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | PROTOPORPHYRIN | PROTOPORPHYRIN | ||
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | ORTHO-PHTHALALDEHYDE | ORTHO-PHTHALALDEHYDE | ||
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | NIMESULIDE | NIMESULIDE | ||
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | BENZYL SALICYLATE | BENZYL SALICYLATE | ||
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | AMPICILLIN TRIHYDRATE | AMPICILLIN TRIHYDRATE | ||
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | NSC-88915 | CHEMBL387152 | 19883083 | |
| 55775 | TDP1 | DRUGGABLE GENOME, ENZYME, DNA REPAIR | NOREPINEPHRINE | NOREPINEPHRINE |
| Page: 1 2 3 4 5 6 7 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |