Please use this identifier to cite or link to this item:
Title: Passing Messages between Biological Networks to Refine Predicted Interactions
Authors: Glass, Kimberly;Huttenhower, Curtis;Quackenbush, John;Yuan, Guo-Cheng
subject: Biology;Computational Biology;Genomics;Genome Analysis Tools;Genetic Networks;Regulatory Networks;Systems Biology;Genetics;Gene Networks;Model Organisms;Yeast and Fungal Models
Year: 2013
Publisher: Public Library of Science
Description: Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at
Standard no: Glass, Kimberly, Curtis Huttenhower, John Quackenbush, and Guo-Cheng Yuan. 2013. “Passing Messages between Biological Networks to Refine Predicted Interactions.” PLoS ONE 8 (5): e64832. doi:10.1371/journal.pone.0064832.
Appears in Collections:HSPH Scholarly Articles

Files in This Item:
Click on the URI links for accessing contents.

Items in HannanDL are protected by copyright, with all rights reserved, unless otherwise indicated.