Bilkent University
Department of Computer Engineering


Activity Analysis in Biological Pathways


Ozgun Babur
Ph.D Student
Computer Engineering Department
Bilkent University

Biological pathway databases collect information on how molecules interact and reactions occur in a cell. Each reaction might have been discovered in a different laboratory under different conditions, using different kinds of cells. Collection of this information builds a cumulative graph of interactions, whose only a subgraph would occur in specific conditions and in specific type of cells. The most popular experimenting system that tells about what happens in the cell in some condition is icroarrays. In microarray experiments, researchers measure expression levels of the genes in the cell, so that we would have an idea on which genes are active and which others are silent. However this is only gene expression data and does not cover post-translational events such as protein modifications which play a major role in cell signaling events. There is a pretty minor literature on identification of the active subgraph of biological pathways using microarray data. One reason is that there is still no established standards for the pathway data in the community. We developed an algorithm which identifies all possible dependency paths in a biological graph which potentially explains dependencies in the gene expressions. Those dependencies would be candidate paths in identification of the active subgraph, which later on would be a good resource for drug development studies.


DATE: November 13, 2006, Monday@ 16:40