Annotating pathways in interaction networks.
Integrating molecular interaction data with existing knowledge of molecular function reveals mechanisms that underly cellular organization. We present NARADA, a software tool that implements a comprehensive analysis suite for functional annotation of pathways. NARADA takes as input a species-specific molecular interaction network and annotation of biomolecules in the network and provides the user with a set of pathways composed of functional attributes, which may be thought of pathway templates in the functional annotation space that recur in various contexts (different groups of specific molecules with similar functional annotation patterns) in the molecular interaction network. NARADA has its underpinnings in formal statistical measures of significance, and algorithmic bases for performance. Comprehensive evaluation on the E. coli transcriptional regulation and proteinprotein interaction data demonstrate NARADA's ability to detect known, as well as novel pathways.
Pandey
Jayesh
J
Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA. jpandey@cs.purdue.edu
Koyutürk
Mehmet
M
Szpankowski
Wojciech
W
Grama
Ananth
A
D000465:Algorithms; D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D005798:Genes, Bacterial; D023281:Genomics / Q000706:statistics & numerical data; D008954:Models, Biological; D015233:Models, Statistical; D008967:Molecular Biology / Q000706:statistics & numerical data*; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data; D012984:Software; D014158:Transcription, Genetic; D014584:User-Computer Interface
D029968:Escherichia coli Proteins