Guan Lab

Department of Computational Medicine & Bioinformatics
Fri, 08/15/2014 - 18:51 -- gyuanfan
TitleModeling Dynamic Functional Relationship Networks and Application to Ex Vivo Human Erythroid Differentiation.
Publication TypeJournal Article
Year of Publication2014
AuthorsZhu F, Shi L, Li H, Eksi R, Engel JDouglas, Guan Y
JournalBioinformatics
Date Published2014 Aug 12
ISSN1367-4811
Abstract

MOTIVATION: Functional relationship networks, which summarize the probability of co-functionality between any two genes in the genome, could complement the reductionist focus of modern biology for understanding diverse biological processes in an organism. One major limitation of the current networks is that they are static while one might expect functional relationships to consistently reprogram during the differentiation of a cell lineage. To address this potential limitation, we developed a novel algorithm that leverages both differentiation stage-specific expression data and large-scale, heterogeneous functional genomic data to model such dynamic changes. We then applied this algorithm to the time-course RNA-Seq data we collected for ex vivo human erythroid cell differentiation.RESULTS: Through computational cross-validation and literature validation, we show that the resulting networks correctly predict the (de)-activated functional connections between genes during erythropoiesis. We identified known critical genes, such as HBD and GATA1, and functional connections during erythropoiesis using these dynamic networks, while the traditional static network was not able to provide such information. Furthermore, by comparing the static and the dynamic networks, we identified novel genes (such as OSBP2 and PDZK1IP1) that are potential drivers of erythroid cell differentiation. This novel method of modeling dynamic networks is applicable to other differentiation processes where time-course genome-scale expression data is available, and should assist in generating greater understanding of the functional dynamics at play across the genome during development. Availability: The network described in this paper is available at http://guanlab.ccmb.med.umich.edu/stageSpecificNetwork.CONTACT: gyuanfan@umich.edu, engel@umich.edu.

DOI10.1093/bioinformatics/btu542
Alternate JournalBioinformatics
PubMed ID25115705