GitHub repository: mmacgilvray18/Phospho_Network
Primary language: GAMS
Created: 2017-04-28T16:14:56Z
Description: This pipeline turns a list of S. cerevesiae phospho-peptides that exhibit stress responsive abundance changes, as measured by mass spectrometry, into a hierarchical signaling network, connecting upstream kinases and phosphatases to their downstream targets. Our computational pipeline is based on the premise that kinases and phosphatases recognize target substrates through specific amino acid sequences at the phosphorylated residue, called phosphorylation motifs. This pipeline groups phospho-peptides with similar abundance changes and the same phosphorylation motif into modules. Modules are partitioned into smaller groups, called submodules, based on differences in phospho-peptide abundance in mutant strain(s) (sources). Candidate submodule regulators, called shared interactors, are identified through enrichment analysis using a protein interaction network in yeast (Chasman et al., 2014). Shared interactor-submodule pairs serve as inputs for a previously developed Integer Programming (IP) approach that connects the sources to their downstream target submodules (Chasman et al., 2014).