Validation of gene regulatory networks from protein-protein interaction data: application to cell-cycle regulation

Authors:
Iti Chaturvedi;Meena Kishore Sakharkar;Jagath C. Rajapakse
Affiliations:
Bioinformatics Research Center, Nanyang Technological University, Singapore and Adams Lab, MAE, Nanyang Technological University, Singapore;Adams Lab, MAE, Nanyang Technological University, Singapore;Bioinformatics Research Center, Nanyang Technological University, Singapore
Venue:
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
Year:
2007

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Abstract

We develop a technique to validate large-scale gene regulatory networks (GRN) by comparing with corresponding protein-protein interaction (PPI) networks. The GRN are obtained with Bayesian networks while PPI networks are obtained from database of known PPI interactions. We look for exact matches and then reduced networks by skipping one or more genes in GRN. We demonstrate our technique on expression profiles of differentially expressed genes in the S. cerevisiae cell cycle. We validate GRNs against a merged database of 53235 genes. The precisions of GRN obtained over all genes were from 0.82 to 0.95 in all the phases. In particular we realized that one-skip and two-skip model significantly improved accuracy of the GRN of different phases of cell cycle.