WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data

BMC Bioinformatics

Table 2 Comparison of major features of WPS with other pathway analysis tools.

	WPS	GenMAPP	Pathway Processor	Cytoscape	PathwayAssist	Ingenuity	MetaCore	PathArt
Customized Pathways or Gene Groups	Yes	Yes	No	?	Yes	Yes	Yes	No
Public Canonical Pathway Collection (e.g. KEGG, BioCarta)	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Color Code Genes with Datasets	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Color Code Pathways (Pathway Tags) with Datasets	Yes	No	No	No	No	No	No	No
Concurrent Visualization of Multiple Datasets (in Colored Pathways/Network)	Yes	No	No	No	No	No	Yes	No
Multiple Datasets Visualization Once a Time (in Colored Pathways/Network)	Yes	No	No	No	Yes	Yes	Yes	Yes
Summarized View of Multiple Pathways (i.e. Pathway Tags)	Yes	No	No	No	No	No	No	No
Pattern Extraction from Data Files	Yes	No	No	No	No	No	No	No
Pattern Extraction from Colored Pathways	Yes	No	No	No	No	No	No	No
Global Enrichment Test (e.g. Fisher's exact test) for a Given List	Yes	No	No	No	No	Yes	No	No
Pathway-Scoped Fisher's exact test for Patterned Genes	Yes	Yes	Yes	No	No	No	No	No
Network View (Gene-Gene Association Network*)	Yes	No	No	Yes	Yes	Yes	Yes	Yes
Network View (Gene-Term Association Network*)	Yes	No	No	No	No	No	No	No
Term-based and Fisher's exact test result-based network filtering**	Yes	No	No	No	No	No	No	No
Sort Whole Dataset into Pathway Scoped Sub-datasets***	Yes	No	No	No	No	No	No	No
Types of Products/Availability (Free to Academic: A; Commercial: C)	A	A	A	A	C	C	C	C

WPS has unique features not found in a single similar application. Seven pathway analysis tools (first row of the table: three of them are free to academic and the other four are commercial products) were selected for comparison of major features (first column of the table) with WPS. The other seven tools for comparison include: GenMAPP [27]; Pathway Processor [29]; Cytoscape [28]; PathwayAssist [23]; Ingenuity: Ingenuity Pathway Analysis tool [25]; MetaCore [26]; PathArt [24].
Yes: has the indicated feature; No: does not have the indicated feature at current time;
?: Not clear.
*: Gene-Term Association Network (GTAN); gene-to-term relation binary network in WPS (can be converted to gene-gene association network too); Gene-Gene Association Network: gene-to-gene relation binary network.
**: Filter a GTAN into a more specific subnetwork with terms user selected and highlighted or with ranked terms from Fisher's exact test result (see Fig. 10, 11, 13, 14)
***: Sort a whole dataset into pathway scoped sub-datasets for further analysis: e.g. batch computation of the sub-datasets for pathway-scoped correlation study.

ISSN: 1471-2105