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Gene: RTF2 |
Gene summary for RTF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RTF2 | Gene ID | 51507 |
| Gene name | replication termination factor 2 | |
| Gene Alias | C20orf43 | |
| Cytomap | 20q13.31 | |
| Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | A0A0A0MQR2 |
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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 |
| 51507 | RTF2 | GSM4909282 | Human | Breast | IDC | 2.16e-05 | 3.63e-01 | -0.0288 |
| 51507 | RTF2 | GSM4909285 | Human | Breast | IDC | 1.03e-06 | 2.22e-01 | 0.21 |
| 51507 | RTF2 | GSM4909286 | Human | Breast | IDC | 4.25e-09 | 2.59e-01 | 0.1081 |
| 51507 | RTF2 | GSM4909293 | Human | Breast | IDC | 1.54e-04 | 2.50e-01 | 0.1581 |
| 51507 | RTF2 | GSM4909295 | Human | Breast | IDC | 1.94e-07 | 4.23e-01 | 0.0898 |
| 51507 | RTF2 | GSM4909298 | Human | Breast | IDC | 2.93e-06 | 2.70e-01 | 0.1551 |
| 51507 | RTF2 | GSM4909301 | Human | Breast | IDC | 8.96e-03 | 3.31e-01 | 0.1577 |
| 51507 | RTF2 | GSM4909304 | Human | Breast | IDC | 2.77e-08 | 3.32e-01 | 0.1636 |
| 51507 | RTF2 | GSM4909305 | Human | Breast | IDC | 6.02e-08 | 3.47e-01 | 0.0436 |
| 51507 | RTF2 | GSM4909306 | Human | Breast | IDC | 7.39e-03 | 2.15e-01 | 0.1564 |
| 51507 | RTF2 | GSM4909308 | Human | Breast | IDC | 8.60e-08 | 2.55e-01 | 0.158 |
| 51507 | RTF2 | GSM4909311 | Human | Breast | IDC | 2.53e-04 | -8.85e-03 | 0.1534 |
| 51507 | RTF2 | GSM4909317 | Human | Breast | IDC | 2.99e-54 | 1.04e+00 | 0.1355 |
| 51507 | RTF2 | GSM4909318 | Human | Breast | IDC | 3.43e-21 | 1.21e+00 | 0.2031 |
| 51507 | RTF2 | GSM4909319 | Human | Breast | IDC | 6.22e-11 | 1.21e-01 | 0.1563 |
| 51507 | RTF2 | GSM4909321 | Human | Breast | IDC | 2.03e-02 | 1.61e-01 | 0.1559 |
| 51507 | RTF2 | brca1 | Human | Breast | Precancer | 1.77e-06 | -1.73e-01 | -0.0338 |
| 51507 | RTF2 | brca2 | Human | Breast | Precancer | 3.66e-05 | -1.73e-01 | -0.024 |
| 51507 | RTF2 | brca3 | Human | Breast | Precancer | 7.79e-05 | -1.73e-01 | -0.0263 |
| 51507 | RTF2 | M2 | Human | Breast | IDC | 4.67e-02 | 4.08e-01 | 0.21 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| 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:00712418 | Breast | Precancer | cellular response to inorganic substance | 26/1080 | 226/18723 | 6.23e-04 | 7.78e-03 | 26 |
| GO:007124113 | Breast | IDC | cellular response to inorganic substance | 29/1434 | 226/18723 | 4.28e-03 | 3.34e-02 | 29 |
| GO:007124123 | Breast | DCIS | cellular response to inorganic substance | 29/1390 | 226/18723 | 2.75e-03 | 2.41e-02 | 29 |
| GO:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:00062612 | Esophagus | ESCC | DNA-dependent DNA replication | 100/8552 | 151/18723 | 2.61e-07 | 3.94e-06 | 100 |
| GO:007124117 | Esophagus | ESCC | cellular response to inorganic substance | 125/8552 | 226/18723 | 2.17e-03 | 9.67e-03 | 125 |
| GO:1902969 | Esophagus | ESCC | mitotic DNA replication | 11/8552 | 14/18723 | 1.30e-02 | 4.27e-02 | 11 |
| GO:00062601 | Liver | HCC | DNA replication | 146/7958 | 260/18723 | 5.68e-06 | 7.02e-05 | 146 |
| GO:007124112 | Liver | HCC | cellular response to inorganic substance | 119/7958 | 226/18723 | 1.26e-03 | 6.92e-03 | 119 |
| GO:0006261 | Liver | HCC | DNA-dependent DNA replication | 80/7958 | 151/18723 | 5.91e-03 | 2.44e-02 | 80 |
| GO:00062606 | Thyroid | PTC | DNA replication | 114/5968 | 260/18723 | 3.09e-05 | 2.95e-04 | 114 |
| GO:0071241110 | Thyroid | PTC | cellular response to inorganic substance | 92/5968 | 226/18723 | 3.01e-03 | 1.49e-02 | 92 |
| GO:000626013 | Thyroid | ATC | DNA replication | 124/6293 | 260/18723 | 1.58e-06 | 1.93e-05 | 124 |
| GO:007124124 | Thyroid | ATC | cellular response to inorganic substance | 98/6293 | 226/18723 | 1.35e-03 | 7.02e-03 | 98 |
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| 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 |
| Page: 1 |
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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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