MAPS: MicroArray processing software for management, data mining and visualization of gene expression data

MAPS is a platform independent software tool that supports the efficient management and the analysis of large amounts of gene expression data across replicated experiments. Its management framework handles input data generated by oligonucleotide arrays. A multi-user environment allows each user to store his/her own data visualization scheme, analysis parameters used, values and formats of the output data. The analysis performs data normalization, data filtering, differential gene expression analysis, co expression analysis in single and/or multiple experiments and classification of unknown samples. Results of expression profiles can be interactively navigated through high quality graphical interfaces and at the same time are automatically stored locally, in ASCII format files for later use. The automatic conversion from array probes to gene names, gene descriptions, gene products (proteins) is achieved through a secure SQL server. Although the tool itself is powerful, the backbone of this approach is a well-curated database of gene sets, i.e., genes that are known to interact in biochemical pathways or molecular signatures. MAPS users can also get any up to date information about microarray probes from TIGR, Unigene, SwissProt, PubMed, Genbank from a dynamic web page that connects MAPS to the BROAD databases.