Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data

Zerrin Isik, Volkan Atalay, Rengul Cetin-Atalay; JMLR W&CP 8:44-54, 2010.

Abstract

In this study, we combined the ChIP-seq and the transcriptome data and integrated these data into signaling cascades. Integration was realized through a framework based on data- and model-driven hybrid approach. An enrichment model was constructed to evaluate signaling cascades which resulted in specific cellular processes. We used ChIP-seq and microarray data from public databases which were obtained from HeLa cells under oxidative stress having similar experimental setups. Both ChIP-seq and array data were analyzed by percentile ranking for the sake of simultaneous data integration on specific genes. Signaling cascades from KEGG pathway database were subsequently scored by taking sum of the individual scores of the genes involved within the cascade. This scoring information is then transferred to en route of the signaling cascade to form the final score. Signaling cascade model based framework that we describe in this study is a novel approach which calculates scores for the target process of the analyzed signaling cascade, rather than assigning scores to gene product nodes.