Pathway Maps of Transcription Factors

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Gene regulation is a process in cells that turns genes on and off at the right place and time. A special type of genes called transcription factors (TFs) carries out this process. TF proteins recognize genes in DNA and make them active or disabled. TFs are very important because all vital parts and activities of cells depend on exact sets of genes being active. However, there are thousands of TFs in humans and other organisms and we still do not know all the genes they regulate. Although scientists are collecting large amounts of information to understand TFs, the collected information is often incomplete and has biases and errors. Analysing many types of evidence about genes and TFs at the same time can overcome these limitations and lead to a wide range of new insights into TF function.******My research program will create computer software to study different types of information that has been collected about TFs, genes and processes in cells. The goal of my work is to build large detailed maps of TFs and processes in cells of humans and other organisms, using statistics and machine learning to merge different types of evidence about gene regulation. These maps will show exactly which genes and cell activities are regulated by any of the known TFs, allowing us to better understand how many different processes in cells work. The maps will reveal new roles of TFs and allow us perform precise laboratory tests to validate these roles. The maps will also help us understand what makes humans unique and similar to other life forms at the cell level. Scientists will also be able to use TF maps to better link information in our genomes to our physical and mental features.******The computer software created in this program will help scientists better re-use information that has been collected in earlier scientific projects, increasing the value of investments in science made by Canadian taxpayers. In the future, the tools developed through this program can be used in many fields. Importantly, the tools are general and can be applied to diverse organisms for which information about genes and TFs is available. For example, once we know how TFs regulate important cell activities in farm animals and crop plants, we can use this knowledge to improve agriculture. The maps will enable more precise, safe modifications of agriculturally important species to produce higher yield and to become more resistant to weather, parasites, and diseases. Once we understand gene regulation of pests and weeds, we will be able to produce more efficient and specific pesticide and herbicide poisons. Similarly, more comprehensive TF knowledge will allow us to specifically change gene regulation in tiny organisms to create safer and environmentally friendly ways of producing chemicals, cleaning up chemical waste, and monitoring air and water for pollution.