Regulon organization of Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Despite the mounting research on Arabidopsis transcriptome and the powerful tools to explore biology of this model plant, the organization of expression of Arabidopsis genome is only partially understood. Here, we create a coexpression network from a 22,746 Affymetrix probes dataset derived from 963 microarray chips that query the transcriptome in response to a wide variety of environmentally, genetically, and developmentally induced perturbations.</p> <p>Results</p> <p>Markov chain graph clustering of the coexpression network delineates 998 regulons ranging from one to 1623 genes in size. To assess the significance of the clustering results, the statistical over-representation of GO terms is averaged over this set of regulons and compared to the analogous values for 100 randomly-generated sets of clusters. The set of regulons derived from the experimental data scores significantly better than any of the randomly-generated sets. Most regulons correspond to identifiable biological processes and include a combination of genes encoding related developmental, metabolic pathway, and regulatory functions. In addition, nearly 3000 genes of unknown molecular function or process are assigned to a regulon. Only five regulons contain plastomic genes; four of these are exclusively plastomic. In contrast, expression of the mitochondrial genome is highly integrated with that of nuclear genes; each of the seven regulons containing mitochondrial genes also incorporates nuclear genes. The network of regulons reveals a higher-level organization, with dense local neighborhoods articulated for photosynthetic function, genetic information processing, and stress response.</p> <p>Conclusion</p> <p>This analysis creates a framework for generation of experimentally testable hypotheses, gives insight into the concerted functions of Arabidopsis at the transcript level, and provides a test bed for comparative systems analysis.</p

explorase: Multivariate Exploratory Analysis and Visualization for Systems Biology

The datasets being produced by high-throughput biological experiments, such as microarrays, have forced biologists to turn to sophisticated statistical analysis and visualization tools in order to understand their data. We address the particular need for an open-source exploratory data analysis tool that applies numerical methods in coordination with interactive graphics to the analysis of experimental data. The software package, known as explorase, provides a graphical user interface (GUI) on top of the R platform for statistical computing and the GGobi software for multivariate interactive graphics. The GUI is designed for use by biologists, many of whom are unfamiliar with the R language. It displays metadata about experimental design and biological entities in tables that are sortable and filterable. There are menu shortcuts to the analysis methods implemented in R, including graphical interfaces to linear modeling tools. The GUI is linked to data plots in GGobi through a brush tool that simultaneously colors rows in the entity information table and points in the GGobi plots.

5AtRabD2b and AtRabD2c have overlapping functions in pollen development and pollen tube growth

<p>Abstract</p> <p>Background</p> <p>Rab GTPases are important regulators of endomembrane trafficking, regulating exocytosis, endocytosis and membrane recycling. Many Rab-like proteins exist in plants, but only a subset have been functionally characterized.</p> <p>Results</p> <p>Here we report that AtRabD2b and AtRabD2c play important roles in pollen development, germination and tube elongation. <it>AtrabD2b </it>and <it>AtrabD2c </it>single mutants have no obvious morphological changes compared with wild-type plants across a variety of growth conditions. An <it>AtrabD2b/2c </it>double mutant is also indistinguishable from wild-type plants during vegetative growth; however its siliques are shorter than those in wild-type plants. Compared with wild-type plants, <it>AtrabD2b/2c </it>mutants produce deformed pollen with swollen and branched pollen tube tips. The shorter siliques in the <it>AtrabD2b/2c </it>double mutant were found to be primarily due to the pollen defects. <it>AtRabD2b </it>and <it>AtRabD2c </it>have different but overlapping expression patterns, and they are both highly expressed in pollen. Both AtRabD2b and AtRabD2c protein localize to Golgi bodies.</p> <p>Conclusions</p> <p>These findings support a partially redundant role for AtRabD2b and AtRabD2c in vesicle trafficking during pollen tube growth that cannot be fulfilled by the remaining AtRabD family members.</p