Given a compounds-forming system, i.e., a system consisting of some compounds and their relationship, can it form a biologically meaningful pathway? It is a fundamental problem in systems biology. Nowadays, a lot of information on different organisms, at both genetic and metabolic levels,
has been collected and stored in some specific databases. Based on these data, it is feasible to address such an essential problem. Metabolic pathway is one kind of compoundsforming systems and we analyzed them in yeast by extracting different (biological and graphic) features from each of
the 13,736 compounds-forming systems, of which 136 are positive pathways, i.e., known metabolic pathway from KEGG; while 13,600 were negative. Each of these compounds-forming systems was represented by 144 features, of which 88 are graph features and 56 biological features. “Minimum
Redundancy Maximum Relevance” and “Incremental Feature Selection” were utilized to analyze these features and 16 optimal features were selected as being able to predict a query compounds- forming system most successfully. It was found through Jackknife cross-validation that
the overall success rate of identifying the positive pathways was 74.26%. It is anticipated that this novel approach and encouraging result may give meaningful illumination to investigate this important topic.
No Supplementary Data
Incremental Feature Selection (IFS);
MaxRel features q;
Minimum redundancy maximum relevance;
Nearest Neighbor Algorithm;
Nearest neighbor algorithm;
local density change;
Document Type: Research Article
Publication date: 2012-01-01
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Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.