title: COMPADRE: an R and web resource for pathway activity analysis by component decompositions.
abstract: The analysis of biological networks has become essential to study functional genomic data. Compadre is a tool to estimate pathway/gene sets activity indexes using sub-matrix decompositions for biological networks analyses. The Compadre pipeline also includes one of the direct uses of activity indexes to detect altered gene sets. For this, the gene expression sub-matrix of a gene set is decomposed into components, which are used to test differences between groups of samples. This procedure is performed with and without differentially expressed genes to decrease false calls. During this process, Compadre also performs an over-representation test. Compadre already implements four decomposition methods [principal component analysis (PCA), Isomaps, independent component analysis (ICA) and non-negative matrix factorization (NMF)], six statistical tests (t- and f-test, SAM, Kruskal-Wallis, Welch and Brown-Forsythe), several gene sets (KEGG, BioCarta, Reactome, GO and MsigDB) and can be easily expanded. Our simulation results shown in Supplementary Information suggest that Compadre detects more pathways than over-representation tools like David, Babelomics and Webgestalt and less false positives than PLAGE. The output is composed of results from decomposition and over-representation analyses providing a more complete biological picture. Examples provided in Supplementary Information show the utility, versatility and simplicity of Compadre for analyses of biological networks.
  
  
  METHODS
  Compadre is freely available at http://bioinformatica.mty.itesm.mx:8080/compadre. The R package is also available at https://sourceforge.net/p/compadre.
authors.affiliation: Cátedra of Bioinformática and Department of Computer Sciences, Tecnológico de Monterrey, Campus Monterrey, Monterrey, Nuevo León, México.
authors.forename: Roberto-Rafael
authors.initials: RR
authors.lastname: Ramos-Rodriguez
authors.forename: Raquel
authors.initials: R
authors.lastname: Cuevas-Diaz-Duran
authors.forename: Francesco
authors.initials: F
authors.lastname: Falciani
authors.forename: Jose-Gerardo
authors.initials: JG
authors.lastname: Tamez-Peña
authors.forename: Victor
authors.initials: V
authors.lastname: Trevino
mesh_terms: D000465:Algorithms; D015870:Gene Expression; D020869:Gene Expression Profiling; D023281:Genomics; D020407:Internet; D025341:Principal Component Analysis; D012984:Software