Mining biological networks for unknown pathways

Biological pathways provide significant insights on the interaction mechanisms of molecules. Presently, many essential pathways still remain unknown or incomplete for newly sequenced organisms. Moreover, experimental validation of enormous numbers of possible pathway candidates in a wet-lab environment is time- and effort-extensive. Thus, there is a need for comparative genomics tools that help scientists predict pathways in an organism‟s biological network. In this paper, we propose a technique to discover unknown pathways in organisms. Our approach makes in-depth use of Gene Ontology (GO)-based functionalities of the enzymes involved in metabolic pathways as follows: (i) Model each pathway as a biological functionality graph of enzyme GO functions, which we call pathway functionality template (PFT). (ii) Locate frequent PF (pathway functionality) patterns so as to infer previously unknown pathways through pattern matching in metabolic networks of organisms. We have experimentally ...

• Type: Journal
• Year: 2007
• Where: BIOINFORMATICS
• Authors: Ali Cakmak, Gultekin Özsoyoglu
• Keywords: BIOINFORMATICS 2007, Biological Pathways, Essential Pathways, Unknown Pathways