Scopes and main features of pathway analysis methodologies and tools.

Each pathway analysis methodology is reported and referred by the first author of the original publication where the pathway analysis methodology and/or tool was presented, followed by the respective reference (column 1); the systems with names in bold (DAVID, SPIA, PATHOME, GGEA and GSEA) are the ones with which the MinePath is compared (section ‘Results’). The publication year is reported in column 2; the third column reports the respective ‘Pathway DBs/schemas’: pathway databases and schemas supported by the tool, where (1) represents KEGG, (2) ReActome, (3) BioCarta, (4) Pathway Commons, (5) WikiPathways, (6) Panther DB, (7) NDEx/PID, (8) MSigDB, (9) sbml, (10) xgmml, (11) BioPax, (12) GPML; the next columns refer to the main functionality offered and the features utilized by the respective method, i.e., ‘G’: Genes, ‘T’: Topology, ‘R’: Regulation, ‘GS’: Gene Selection, ‘PS’: Pathway Selection, ‘SPS’: Sub-Path Selection, ‘W’: Web-based, ‘Vg’: Visualization support using genes color coding, ‘Vi’: Interaction features of the visualization, ‘Vr’: Visualization support using relations color coding.