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Table 2 Known implementation of the methods provided in ToPASeq

From: ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data

Method Language Source Pathways Format Input data Methods Issusses
topologyGSA R Bioconductor one example graphNEL GEDM topologyGSA too computationaly intense
clipper R Bioconductor imported from graphite pathway GEDM clipper two separate steps necessary
DEGraph R Bioconductor parsing function for KGML graphNEL GEDM DEGraph  
SPIA R Bioconductor parsing function for KGML, H. sapiens and M. musculus pre-parsed list of adjacency matrices DEG and log fold-changes SPIA Only for EntrezGene IDs
PRS tool MATLAB web a KEGG unknown GEDM PRS can not add or modify pathways, the data must have manufacturer probeset IDs, limited set of: possible platforms, DE tests,
PWEA C++ web b human pathways from KEGG unknown GSD PWEA only for UNIX-like
TAPPA Java web c KEGG or PPI added to a gene set - - TAPPA not available
graphite R Bioconductor pathways for 14 species from up to 6 databases Pathway depends on the method topologyGSA, clipper, SPIA, DEGraph, suboptimal import of the methods
  1. a - http: //www.buckingham.ac.uk/research/clore-laboratory-diabetes-obesity-and-metabolic-research/staff/maysson-al-haj-ibrahim/prs-tool/ b - http://zlab.bu.edu/PWEA/index.php c - http://watson.mcgee.mcw.edu:8080/~sgao, the page is down. (First accessed 4 Apr 2012) PPI - protein-protein interactions GEDM - gene expression data matrix, log2-transformed and normalized expression profiles