Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana

Ana Pop,Anjali Iyer-Pascuzzi,Olga G Troyanskaya,Curtis Huttenhower,Philip N Benfey

doi:10.1186/1752-0509-4-180

Abstract

BackgroundRecent years have seen an explosion in plant genomics, as the difficulties inherent in sequencing and functionally analyzing these biologically and economically significant organisms have been overcome. Arabidopsis thaliana, a versatile model organism, represents an opportunity to evaluate the predictive power of biological network inference for plant functional genomics.ResultsHere, we provide a compendium of functional relationship networks for Arabidopsis thaliana leveraging data integration based on over 60 microarray, physical and genetic interaction, and literature curation datasets. These include tissue, biological process, and development stage specific networks, each predicting relationships specific to an individual biological context. These biological networks enable the rapid investigation of uncharacterized genes in specific tissues and developmental stages of interest and summarize a very large collection of A. thaliana data for biological examination. We found validation in the literature for many of our predicted networks, including those involved in disease resistance, root hair patterning, and auxin homeostasis.ConclusionsThese context-specific networks demonstrate that highly specific biological hypotheses can be generated for a diversity of individual processes, developmental stages, and plant tissues in A. thaliana. All predicted functional networks are available online at http://function.princeton.edu/arathGraphle.

Highlights

Recent years have seen an explosion in plant genomics, as the difficulties inherent in sequencing and functionally analyzing these biologically and economically significant organisms have been overcome
Overview of integrated functional networks inferred for A. thaliana pathways, tissues, and developmental stages We generated a range of networks (Table 1) addressing questions of increasing specificity regarding A. thaliana gene pair relationships
We found that the transcription factors (TFs) MAGPIE (MGP), NUTCRACKER (NUC) and JACKDAW (JKD) are co-active in the seedling growth stage, while MGP and NUC are co-active in the root development stages

Summary

Introduction

Recent years have seen an explosion in plant genomics, as the difficulties inherent in sequencing and functionally analyzing these biologically and economically significant organisms have been overcome. Arabidopsis thaliana, a versatile model organism, represents an opportunity to evaluate the predictive power of biological network inference for plant functional genomics. Arabidopsis thaliana is the most common model organism for plants, with a short life cycle, relatively few genes, and a fully sequenced genome [2]. It is a multicellular organism with multiple tissue types and developmental stages, and much of its tissue-specific and stage-specific molecular biology has yet to be determined.

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Conclusion