Development of modular software for the analysis of genic expression

• Grant number: 03/02103-0
• Support Opportunities: Research Grants - Innovative Research in Small Business - PIPE
• Start date: June 01, 2004
• End date: February 28, 2005
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computer Systems
• Principal Investigator: Daniel Oliveira Dantas
• Grantee: Daniel Oliveira Dantas
• Company: Sunset Informática Ltda
• City: São Paulo

Abstract

This project aims to develop a piece of modular software for the analysis of genic expression, measured by microarrays, membrane arrays, sage or other techniques. The software should be composed of the following modules: image analysis; database; normalization; clustering, and reduction of dimensionality. The image analysis module permits the measurement of expression based on microarray images or membrane array. The database module stores the architecture of the analyzed chip, the genes associated with each spot and permits the organization and retrieval of information from several related experiments. As the name itself indicates, the normalization module attributes measurements for various experiments with the same reference, making it possible in this way to compare results. The clustering module makes possible the grouping of similar signals, obtained in experiments of temporal expression measurement or progressive, increasing or decreasing stress. The reduction of dimensionality permits the discovery of a minimum gene set, the signal of which makes it possible to differentiate at least two biological states of interest. This software offers some innovative characteristics compared to other known programs, among which: the method of image analysis is based on a technique of precise segmentation of the spots; the databases can store families of experiments and not just one experiment, as is the norm; the procedures of reduction of dimensionality applied are innovate techniques developed by the group itself. (AU)