title: Uncovering the rules for protein-protein interactions from yeast genomic data.
abstract: Identifying protein-protein interactions is crucial for understanding cellular functions. Genomic data provides opportunities and challenges in identifying these interactions. We uncover the rules for predicting protein-protein interactions using a frequent pattern tree (FPT) approach modified to generate a minimum set of rules (mFPT), with rule attributes constructed from the interaction features of the yeast genomic data. The mFPT prediction accuracy is benchmarked against other commonly used methods such as Bayesian networks and logistic regressions under various statistical measures. Our study indicates that mFPT outranks other methods in predicting the protein-protein interactions for the database used. We predict a new protein-protein interaction complex whose biological function is related to premRNA splicing and new protein-protein interactions within existing complexes based on the rules generated. Our method is general and can be used to discover the underlying rules for protein-protein interactions, genomic interactions, structure-function relationships, and other fields of research.
authors.affiliation: State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China. jin.wang.1@stonybrook.edu
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
authors.forename: Chunhe
authors.initials: C
authors.lastname: Li
authors.forename: Erkang
authors.initials: E
authors.lastname: Wang
authors.forename: Xidi
authors.initials: X
authors.lastname: Wang
mesh_terms: D016681:Genome, Fungal / Q000235:genetics*; D008928:Mitochondria / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D012372:ROC Curve; D012270:Ribosomes / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
chemical_list: D029701:Saccharomyces cerevisiae Proteins