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Research: Project

A data-integrative systems biology study of the gene-regulatory network driving flowering in Arabidopsis

Miguel Godinho, BIOBASE, Wolfenbüttel

BIOBASE has a large repertoire of databases and computational tools that can be applied to the exploration of mechanisms regulating flowering and seed development.

ExPlain™ is a data analysis system that combines promoter and pathway analysis tools. Those tools are integrated in a computational workflow that starts with the storage of microarray, RNA-seq, or ChIP-seq data. The workflow leads to the identification of transcription factors associated with the initial data, and to predictions on how combinations of those transcription factors can induce the observed gene expression patterns.

Simultaneously, the SYSFLO network is producing experimental datasets, data analysis algorithms, and models pertaining the flower development in the model plant Arabidopsis.

One of my tasks is to create mechanisms for the integration of those deliverables with BIOBASE products. Good integration mechanisms have the potential of contributing to a) the expansion of the knowledge stored in our databases, b) more efficient workflows, and c) more effective database querying systems.

After gaining a deep knowledge on the various databases and bioinformatic tools available in-house, with special focus on what concerns gene regulation mechanisms, I’m expanding ExPlain™ so that the tools there assembled can exchange data with other web-based information systems.

At the core of the expansion, is the development of a REST based web-services integration layer. The initial application of the integration layer will be the coupling of ExPlain™ with PRI-CAT, a web-tool for the analysis, storage, and visualization of plant ChIP-seq experiments, developed by the SYSFLO partner Plant Research International.

Still in the context expanding ExPlain™, and at a more exploratory level, I’m developing a module that permits the storage, exploration, and visualization of genome-scale metabolic networks. Flux Balance Analysis is a constraint-based modelling approach for the prediction of the distribution of fluxes in a metabolic network. Two FBA-based metabolic models for Arabidopsis thaliana can be already found in the literature. The integration of those models brings additional information to support the analysis of regulatory pathways.

At the end of the project I'm expected to be equipped with a valuable set of transferable skills, result of the various SYSFLO actions on that domain, a broad knowledge on the various techniques used to study homeosis, and a strong experience on developing innovative approaches for data integration.

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