DBYeast: Infrastructure and algorithms for analysis and identification of gene regulatory networks

Principal Investigator of the IST team: Isabel Sá-Correia

Contract: POSI/EIA/57398/2004

Start date: 01/01/2005

Duration: 36 months


Living organisms are extraordinarily complex systems that are now being studied in a completely new fashion, and in a detail never contemplated before. Recent advances in  biology have shown that both the functioning and the development of living organisms are controlled by interaction networks between genes, proteins and other small molecules.
These biochemical networks may represent protein-protein interactions, the metabolism or the system of gene regulation of an organism, and even mixed networks that contain information coming from some of the previous sources. The prime objective of this project is to study interaction networks and their underlying complexity, focusing on gene regulation networks. Research will be centered on unveiling the gene regulatory mechanisms of a simple organism, the yeast (Saccharomyces cerevisiae), extensively used by the scientific community as an experimental platform. In order to accurately model and explore the interaction networks inherent to this biological system, significant advances are required in several aspects of mathematical and algorithmic theory.
Addressing such problems represents the second goal of the present proposal. The project is organized into five tasks. The first task is focused on providing a publicly available web-based database, that includes all available information on gene regulation data off the yeast organism. The second task is aimed at devising new algorithms for motif inference based on an accurate model for transcriptional DNA sequence signals. The third task is devoted to the development of biclustering algorithms for gene expression analysis, obtained from microarray data and quantitative proteomics. The fourth task is the integration into an information system of the computational tools obtained in the previous tasks, and will support the work of researchers interested in genomics and regulatory networks. The fifth task is a practical test of system, achieved by using it the analysis of genome-wide expression results. Given the interdisciplinary nature of the endeavour, this project brings together specialists from computer science (Knowledge
Discovery and Bioinformatics - KDBIO and and HELIX / Inria Rhône-Alpes) and biology (Biological Sciences Research Group – BSRG). The KDBIO group will focus on the algorithmic aspects of the problem, applying their expertise in inductive inference and data mining techniques to the extraction of knowledge from genome sequence information and experimental gene activation data. The BSRG group will contribute with their knowledge in the biological issues, leveraging the algorithmic contributions of the KDBIO group. Aside from these two groups, the proposed research will be pursued in cooperation with top international research centers, in some cases as a byproduct of ongoing cooperation work. It is worthwhile stressing that the proposed project provides an important opportunity for making significant contributions in a fruitful and modern topic that Portugal cannot risk leaving behind.