Bioconductor’s SPIA package

This package implements the Signaling Pathway Impact Analysis (SPIA) algorithm described in Tarca et al. (2009), Khatri et al. (2007) and Draghici et al. (2007). SPIA uses the information from a set of differentially expressed genes and their fold changes, as well as pathways topology in order to assess the significance of the pathways in the condition under the study. The current version of SPIA algorithm includes out-of-date KEGG signaling pathway data for hsa and mmu organisms for illustration purposes. However, the current version of the package includes functionality to generate the required up-to-date processed pathway data from KEGG xml (KGML) files that licensed users can download for the organism of interest from KEGG’s ftp site. Also, these files can be downloaded individualy using the Dowload KEGML button from each pathway’s web page. The pathways that will be processed and analyzed for a given organism are those i) containing at least one relation between genes/proteins considered by SPIA, and ii) having no reactions. The outdated KEGG data that was preprocessed for SPIA analysis and is included for the hsa and mmu organisms was downloaded from KEGG’s website on: 09/07/2012. For a list of changes in SPIA compared to previous versions see the last section in this document.