Project Details
Abstract
Creating a tool to display the cancer-related genes with gene regulation (2nd year)) In our previous study, we have created a cancer-related genes database (CRGD). In this database, many biomarker potential genes were identified. In this study, we will try to create a tool to display cancer-related genes with gene regulation based on the CRGD and public databases, such as NCBI and GeneCards. This tool will let researchers or physicians retrieve the cancer-related genes with gene regulation easily and quickly. A text mining program, BioRAT, will be used to retrieve reports that describe cancer-related genes and gene regulation. If a report of cancer-related gene with up regulation is found, the gene will be annotated as “gene name(u)”. If a report of cancer-related gene with down regulation is found, the gene will be annotated as “gene name(d)”. With the same idea, the gene will be annotated as “gene name(b)” for both up and down regulations reported, and “gene name(e)” for equivocal regulation. After cancer-related genes with gene regulation are identified, we will create a tool using the HTML (HyperText Markup Language) to display the cancer-related genes with gene regulation on web pages for researchers. These genes will then be traced to its gene family according to the public gene family databases, such as HGNC, TAIR and Genetic Home Reference. After a user input a cancer name on the tool, many gene grids will be produced on the web page. One grid stands for one gene family. One gene family with its cancer-related genes will be placed in one grid. A gene family is a set of genes defined by presumed homology, i.e. evidence that the genes evolved from a common ancestral gene. They generally share some biochemical activity. Genes are generally categorized into families based upon shared sequence motifs and similarities in structure. In the first year, we have created a tool to display the bladder cancer-related genes with gene regulation and its gene families. In the 2nd and 3rd years, we will complete the tool for 32 cancers using the same model. Using this tool, biological researches or clinical physicians can retrieve the cancer-related genes with gene regulation and its gene families quickly. It can help researchers understand how genes are related to each other in cancers. This tool can also help researchers and physicians to search biomarkers for cancer study.
Project IDs
Project ID:PC10012-0003
External Project ID:NSC100-2218-E182A-001
External Project ID:NSC100-2218-E182A-001
Status | Finished |
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Effective start/end date | 01/11/11 → 31/10/12 |
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