When St. Jude chair of Computational Biology Jinghui Zhang, Ph.D., and her colleagues created the ProteinPaint web tool, their aim was to organize just such a mass of data as Michael Dyer, Ph.D., chair of the St. Jude Department of Developmental Neurobiology, and his colleagues have generated in mapping the epigenetics of retinal cell development.
Created in 2015, ProteinPaint gives researchers an easy-to-use interactive visual interface to enable them to zero in on mutations in genes that cause cancer, and to explore those mutations, their clinical effects and the scientific papers published on them.
Said Dyer of ProteinPaint, "St. Jude has envisioned this resource as a one-stop shop for researchers studying childhood cancers. Having our data there is going to be enormously useful to the community of researchers studying retinal development, retinoblastoma and other retinal diseases.
"It's a huge global community," he said. "For example, the largest vision conference has over 10,000 participants each year from more than 75 countries. Until now, epigenetic studies of retinal development have been largely piecemeal. The dataset we generated on retinal epigenetics is the most comprehensive to date. And it's particularly powerful because it encompasses both mouse and human epigenetics.
"Using the ProteinPaint web portal, a scientist can just type in a target gene and in seconds get the complete epigenetic landscape of that gene during development and in retinoblastoma.
"Without ProteinPaint, researchers would have to go to a public repository where the raw data was deposited and transfer scores of large files to their computer. Then, they would have to use a search program to somehow find what they were looking for and visualize the result. Not many researchers have the capability of doing that."
The retinal epigenetic data is available on the ProteinPaint web site. ProteinPaint is part of the pediatric cancer PeCan data portal, which offers interactive access to an ever-growing trove of data on cancer mutations from research projects at St. Jude and its collaborators.