IBR   13079
INSTITUTO DE BIOLOGIA MOLECULAR Y CELULAR DE ROSARIO
Unidad Ejecutora - UE
congresos y reuniones científicas
Título:
A novel tool to compare microarray data from different experiments
Autor/es:
KURTH, D.G.; DAURELIO, L.D.; ORELLANO, E.G.; ESTEBAN, L.
Lugar:
Córdoba
Reunión:
Congreso; 2do Congreso Argentino de Bioinformática y Biología Computacional; 2011
Institución organizadora:
Asociación Argentina de Bioinformática y Biología Computacional
Resumen:
DNA microarrays enable the transcript levels of an entire genome to be measured simultaneously. Recent improvements in array manufacture, sample preparation, and data analysis are shifting emphasis from the technology itself to experimental design and the broader range of biological questions that can be addressed. The past year has also seen a transition from experiments involving a small number of conditions, with an emphasis on the specific genes induced or repressed, to experiments involving hundreds of conditions in which patterns of global gene expression are used to classify disease specimens and discover gene functions and drug targets. Basic research, medicine, and pharmacology are all likely to benefit from these advances. The rapid advances in biotechnology have given rise to a variety of high-dimensional data techniques. Many of these, including DNA microarray experiments, generate great numbers of data. Microarrays are available for diverse organism, including several which have not accessible their genome sequence or basic tools for data analysis. On the other hand sometimes is necessary to compare the data obtained in different experiments. In this context, program designed to resolve these situation are required.A simple Perl script was developed to compare results obtained in different experiments for the same chip platform. The script was created to analyze the results obtained from microarray experiments using a cDNA microarrays platform (Martinez-Godoy et al. 2008) of citrus plants exposed to diverse biotic stresses. The result for each assay are tab-delimited text file with an spot or EST identifier (ID) and its associated parameters for all the microarray spots.Next, differentially expressed genes are extracted and they can be functionally grouped using their respective Arabidopsis thaliana orthologous genes.The script searches for particular groups of genes, requested from the user, comparing them between different experiments. The input file could be a citrus ID list or an Arabidopsis identifier (ATG) list, and the user is allowed to choose which parameters will be returned. The output file contains the ID/ATG and the selected parameters for each experiment. An user friendly web interface allow to this tool to be more handy. Considering generally the results obtained by oomics techniques, simple modifications of this script will make possible similar comparison between experiments obtained with the same platform.Reference List: Martinez-Godoy M.A. et al. (2008) A genome-wide 20 K citrus microarray for gene expression analysis. BMC.Genomics9, 318.