%0 Journal Article %J Genomics %D 2008 %T Direct functional assessment of the composite phenotype through multivariate projection strategies %A A. Conesa %A Bro, R. %A Garcia-Garcia, F. %A Prats, J. M. %A Gotz, S. %A Kjeldahl, K. %A Montaner, D. %A Dopazo, J. %K Breast Neoplasms/genetics Computational Biology/*methods Databases %K Genetic Female Gene Expression Profiling/*statistics & numerical data Humans Mathematical Computing Multivariate Analysis Phenotype %X

We present a novel approach for the analysis of transcriptomics data that integrates functional annotation of gene sets with expression values in a multivariate fashion, and directly assesses the relation of functional features to a multivariate space of response phenotypical variables. Multivariate projection methods are used to obtain new correlated variables for a set of genes that share a given function. These new functional variables are then related to the response variables of interest. The analysis of the principal directions of the multivariate regression allows for the identification of gene function features correlated with the phenotype. Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches.

%B Genomics %V 92 %P 373-83 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18652888 %0 Journal Article %J Nucleic Acids Res %D 2008 %T GEPAS, a web-based tool for microarray data analysis and interpretation %A Tarraga, J. %A Medina, Ignacio %A Carbonell, J. %A Huerta-Cepas, J. %A Minguez, P. %A Alloza, E. %A Fatima Al-Shahrour %A Vegas-Azcarate, S. %A Goetz, S. %A Escobar, P. %A Garcia-Garcia, F. %A A. Conesa %A Montaner, D. %A Dopazo, J. %K gepas %K microarray data analysis %X

Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org.

%B Nucleic Acids Res %V 36 %P W308-14 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18508806