Pathways Reconstruction

Gal Chechik

The set of cellular metabolic reactions forms a complex network of interactions, but even in well studied organisms the resulting pathways contain many unidentified enzymes. We study how 'structural' relations between genes in the yeast metabolic pathway are manifested in functional properties of genes and their products, including mRNA expression, protein domain content and cellular localizations. We develop compact and interpretable probabilistic models for representing protein-domain co-occurrences and gene expression time courses. The former can provide predictions relating domains and gene functions. The latter reveals relations between the activation of genes and the usage of their protein products in the pathways. These models are then combined and used for completing unidentified enzymes in the pathways, achieving accuracy that is significantly superior to existing state-of-the-art approaches.

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