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Gene: TOPBP1 |
Gene summary for TOPBP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TOPBP1 | Gene ID | 11073 |
| Gene name | DNA topoisomerase II binding protein 1 | |
| Gene Alias | Dpb11 | |
| Cytomap | 3q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000075 | UniProtAcc | A0AV47 |
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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 |
| 11073 | TOPBP1 | CA_HPV_3 | Human | Cervix | CC | 3.17e-02 | 5.37e-02 | 0.0414 |
| 11073 | TOPBP1 | CCI_1 | Human | Cervix | CC | 9.43e-03 | 5.64e-01 | 0.528 |
| 11073 | TOPBP1 | CCI_2 | Human | Cervix | CC | 1.10e-08 | 9.96e-01 | 0.5249 |
| 11073 | TOPBP1 | CCI_3 | Human | Cervix | CC | 5.29e-12 | 7.92e-01 | 0.516 |
| 11073 | TOPBP1 | sample3 | Human | Cervix | CC | 2.35e-02 | 2.18e-01 | 0.1387 |
| 11073 | TOPBP1 | T3 | Human | Cervix | CC | 1.78e-06 | 2.05e-01 | 0.1389 |
| 11073 | TOPBP1 | LZE2T | Human | Esophagus | ESCC | 7.88e-12 | 1.35e+00 | 0.082 |
| 11073 | TOPBP1 | LZE4T | Human | Esophagus | ESCC | 1.01e-08 | 3.27e-01 | 0.0811 |
| 11073 | TOPBP1 | LZE5T | Human | Esophagus | ESCC | 5.63e-04 | 3.54e-01 | 0.0514 |
| 11073 | TOPBP1 | LZE7T | Human | Esophagus | ESCC | 9.73e-04 | 4.71e-01 | 0.0667 |
| 11073 | TOPBP1 | LZE20T | Human | Esophagus | ESCC | 5.07e-04 | 1.29e-01 | 0.0662 |
| 11073 | TOPBP1 | LZE22T | Human | Esophagus | ESCC | 9.71e-06 | 4.30e-01 | 0.068 |
| 11073 | TOPBP1 | LZE24T | Human | Esophagus | ESCC | 4.67e-18 | 4.99e-01 | 0.0596 |
| 11073 | TOPBP1 | P1T-E | Human | Esophagus | ESCC | 2.10e-04 | 4.44e-01 | 0.0875 |
| 11073 | TOPBP1 | P2T-E | Human | Esophagus | ESCC | 6.83e-73 | 1.36e+00 | 0.1177 |
| 11073 | TOPBP1 | P4T-E | Human | Esophagus | ESCC | 6.62e-29 | 7.72e-01 | 0.1323 |
| 11073 | TOPBP1 | P5T-E | Human | Esophagus | ESCC | 2.18e-21 | 4.57e-01 | 0.1327 |
| 11073 | TOPBP1 | P8T-E | Human | Esophagus | ESCC | 1.95e-29 | 5.72e-01 | 0.0889 |
| 11073 | TOPBP1 | P9T-E | Human | Esophagus | ESCC | 3.08e-11 | 3.03e-01 | 0.1131 |
| 11073 | TOPBP1 | P10T-E | Human | Esophagus | ESCC | 5.57e-39 | 7.65e-01 | 0.116 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:00447725 | Cervix | CC | mitotic cell cycle phase transition | 89/2311 | 424/18723 | 2.70e-07 | 1.12e-05 | 89 |
| GO:00073466 | Cervix | CC | regulation of mitotic cell cycle | 88/2311 | 457/18723 | 1.26e-05 | 2.60e-04 | 88 |
| GO:19019903 | Cervix | CC | regulation of mitotic cell cycle phase transition | 63/2311 | 299/18723 | 1.27e-05 | 2.60e-04 | 63 |
| GO:00093149 | Cervix | CC | response to radiation | 86/2311 | 456/18723 | 3.50e-05 | 5.63e-04 | 86 |
| GO:19019873 | Cervix | CC | regulation of cell cycle phase transition | 74/2311 | 390/18723 | 9.80e-05 | 1.27e-03 | 74 |
| GO:00102126 | Cervix | CC | response to ionizing radiation | 34/2311 | 148/18723 | 2.23e-04 | 2.53e-03 | 34 |
| GO:00448392 | Cervix | CC | cell cycle G2/M phase transition | 31/2311 | 148/18723 | 2.07e-03 | 1.51e-02 | 31 |
| GO:00457862 | Cervix | CC | negative regulation of cell cycle | 67/2311 | 385/18723 | 2.21e-03 | 1.59e-02 | 67 |
| GO:00000862 | Cervix | CC | G2/M transition of mitotic cell cycle | 29/2311 | 137/18723 | 2.40e-03 | 1.70e-02 | 29 |
| GO:00062602 | Cervix | CC | DNA replication | 48/2311 | 260/18723 | 2.70e-03 | 1.85e-02 | 48 |
| GO:00459302 | Cervix | CC | negative regulation of mitotic cell cycle | 44/2311 | 235/18723 | 3.02e-03 | 1.99e-02 | 44 |
| GO:00427705 | Cervix | CC | signal transduction in response to DNA damage | 34/2311 | 172/18723 | 3.52e-03 | 2.27e-02 | 34 |
| GO:19019912 | Cervix | CC | negative regulation of mitotic cell cycle phase transition | 35/2311 | 179/18723 | 3.73e-03 | 2.38e-02 | 35 |
| GO:00109482 | Cervix | CC | negative regulation of cell cycle process | 51/2311 | 294/18723 | 7.35e-03 | 3.94e-02 | 51 |
| GO:004477216 | Esophagus | ESCC | mitotic cell cycle phase transition | 281/8552 | 424/18723 | 4.63e-18 | 4.45e-16 | 281 |
| GO:000734615 | Esophagus | ESCC | regulation of mitotic cell cycle | 293/8552 | 457/18723 | 8.00e-16 | 5.64e-14 | 293 |
| GO:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:001021217 | Esophagus | ESCC | response to ionizing radiation | 110/8552 | 148/18723 | 1.11e-12 | 4.78e-11 | 110 |
| GO:190198713 | Esophagus | ESCC | regulation of cell cycle phase transition | 242/8552 | 390/18723 | 3.86e-11 | 1.26e-09 | 242 |
| GO:000931419 | Esophagus | ESCC | response to radiation | 277/8552 | 456/18723 | 4.42e-11 | 1.43e-09 | 277 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| TOPBP1 | SNV | Missense_Mutation | c.4048N>C | p.Glu1350Gln | p.E1350Q | Q92547 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TOPBP1 | SNV | Missense_Mutation | c.1984N>C | p.Glu662Gln | p.E662Q | Q92547 | protein_coding | deleterious(0) | benign(0.08) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TOPBP1 | SNV | Missense_Mutation | rs768252230 | c.2099N>A | p.Arg700His | p.R700H | Q92547 | protein_coding | deleterious(0) | possibly_damaging(0.56) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TOPBP1 | SNV | Missense_Mutation | rs74738463 | c.82N>A | p.Glu28Lys | p.E28K | Q92547 | protein_coding | deleterious(0.02) | benign(0.031) | TCGA-BH-A0BL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| TOPBP1 | SNV | Missense_Mutation | c.3781C>T | p.His1261Tyr | p.H1261Y | Q92547 | protein_coding | tolerated(0.36) | benign(0.377) | TCGA-BH-A0DX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
| TOPBP1 | SNV | Missense_Mutation | c.674N>G | p.His225Arg | p.H225R | Q92547 | protein_coding | deleterious(0) | possibly_damaging(0.84) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TOPBP1 | SNV | Missense_Mutation | c.3421N>C | p.Glu1141Gln | p.E1141Q | Q92547 | protein_coding | tolerated(0.09) | possibly_damaging(0.898) | TCGA-BH-A18K-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| TOPBP1 | SNV | Missense_Mutation | c.2351A>G | p.Asn784Ser | p.N784S | Q92547 | protein_coding | deleterious(0.04) | possibly_damaging(0.541) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| TOPBP1 | SNV | Missense_Mutation | novel | c.2183N>A | p.Gly728Glu | p.G728E | Q92547 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A5IZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| TOPBP1 | SNV | Missense_Mutation | c.778C>A | p.His260Asn | p.H260N | Q92547 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
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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 |
| Page: 1 |
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