Hi my name is Carly Hom and I am an undergraduate student researcher at Arizona State University working with Dr. Karmella Haynes. In my current lab I am using Synthetic Biology and Bioinformatics to investigate reliable and predictable reactivation of dormant genes that can help treat cancer and enable tissue re-growth. By determining which silenced genes will switch to an active state in osteosarcoma cells, with the presence of the synthetic transcription factor PC-TF, my work will establish a comprehensive method for predicting the effect of rationally designed protein-based drugs. Pc-TF, a synthetic transcription factor developed by Dr. Haynes, regulates cell states by binding the repressive trimethyl-histone H3 lysine 27 signal (H3K27me3) and switching silenced genes to an active state in osteosarcoma cells. Since a comprehensive ChIP map is not available for osteosarcoma, I will be identifying genes associated with H3K27me3 in liver (HepG2) and fibroblast (BJ) cell lines. Overall, I will need to collect about 1000 genes from the ENCODE database that show a significant enough H3K27me3 signal at the promoter of the gene. I have already figured out how to project only information from the HepG2 and BJ cell lines in relation to H3K27me3, but by just clicking to move through the cell line to find genes will take entirely too long and can cause me to miss important genes. At the request of Dr. Haynes I am asking if ENCODE has some sort of filter program that will provide a list of genes where the promoter site shows a high level of the H3K27me3 histone methylation. I will need it to be able to find the beginning of the gene's promoter on the UCSC Genome Browser and then show about 500bps to the left and 500bps to the right of the promoter . Ultimately, I want to be able to navigate through the genes in this cell line that show a significant enough H3K27me3 signal at the promoter (everything else with a low H3K27me3 signal I do not care about). If you could get back to me on whether this is even possible to do within the Genome Browser, and if yes, how I would be able to do this that would be great. Thank you!
- Carly Hom -- Caroline Hom Tempe, AZ Ph: 602-315-5728 Arizona State University Ira A. Fulton Schools of Engineering Biomedical Engineering _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
