Communications of the ACM
Computer Scientists Present New Method to Reconstruct Signaling Pathways
Scientists at Virginia Polytechnic Institute and State University have developed an algorithm that can reconstruct signaling pathways from a background network of molecular interactions.
Credit: Life Sciences Research
Researchers at Virginia Polytechnic Institute and State University (Virginia Tech) have developed a new computational algorithm that automatically reconstructs signaling pathways from a background network of molecular interactions.
Signaling pathways are networks of molecules in a cell that work together to control a cell's response to its environment. Understanding their nature is an important part of biomedical research and can provide more insight into how cancer cells live or die.
The algorithm, called PathLinker, starts by identifying receptors and transcription factors in a specific pathway and then reconstructs that pathway by finding multiple short paths in the background network that connect receptors to transcription factors.
The researchers checked PathLinker against comprehensive gold-standard sets of signaling pathways in existing, manually curated databases, and found it to be extremely accurate.
PathLinker is designed to find the best route a cell might use to transfer the signal and all alternate routes. Even the "mistakes" it makes may point to proteins and interactions that have not yet been assigned to a specific signaling pathway, according to Reed College professor Anna Ritz, who led the PathLinker research effort while a post-doctoral fellow at Virginia Tech.
From Virginia Tech News
View Full Article
Abstracts Copyright © 2016 Information Inc., Bethesda, Maryland, USA
No entries found