title: Graphite Web: Web tool for gene set analysis exploiting pathway topology.
abstract: Graphite web is a novel web tool for pathway analyses and network visualization for gene expression data of both microarray and RNA-seq experiments. Several pathway analyses have been proposed either in the univariate or in the global and multivariate context to tackle the complexity and the interpretation of expression results. These methods can be further divided into 'topological' and 'non-topological' methods according to their ability to gain power from pathway topology. Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges. To this day, the most used approaches are non-topological and univariate although they miss the relationship among genes. On the contrary, topological and multivariate approaches are more powerful, but difficult to be used by researchers without bioinformatic skills. Here we present Graphite web, the first public web server for pathway analysis on gene expression data that combines topological and multivariate pathway analyses with an efficient system of interactive network visualizations for easy results interpretation. Specifically, Graphite web implements five different gene set analyses on three model organisms and two pathway databases. Graphite Web is freely available at http://graphiteweb.bio.unipd.it/.
authors.affiliation: Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Sales
authors.forename: Enrica
authors.initials: E
authors.lastname: Calura
authors.forename: Paolo
authors.initials: P
authors.lastname: Martini
authors.forename: Chiara
authors.initials: C
authors.lastname: Romualdi
mesh_terms: D000818:Animals; D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D012984:Software