BiologicalNetworks 2.0 - an integrative view of genome biology data

BMC Bioinformatics

Table 1 Web-accessible tools for microarray pathway and DNA sequence regulation analysis.

Features/Tools		GG	PS	ST	IN	PA	CS	GE	VS	GX	TV	PP	BN
Pathway/Networks	Curated Pathways Content	+	+	-	+	-	-	-	-	-	-	+/-	+/-
	Biological Themes/Functional Enrichment	+	-	-	+	-	+	-	+	-	-	-	+
	Build Pathways/Networks inference	+	+	+	-	-	+	+	+	-	-	-	+
Microarray	Multi-Experiment Support	-	+	-	+	+	-	-	-	+	+	+	+
	Search of Public Expression Compendiums	-	-	-	-	+	-	-	-	+/-	+/-	+	+
	Microarray-Pathway-Sequence Integration	-	-	-	-	+	+/-	-	-	+/-	+/-	-	+
DNA Sequences	General	+/-	-	+	-	+	-	+	-	+	+	+	+
	Gene Regulation	+	-	+	-	+	-	+	-	+/-	+/-	+	+
	Regulatory regions	-	-	-	-	+	-	+	-	+/-	+/-	-	+
	Sequence search	-	-	-	-	-	-	+	-	+	+	+	+/-
	Sequence Annotation	-	-	-	-	-	-	+	-	-	-	-	+/-
Comparative Genomics	Homology Search	-	-	+	-	+	-	+	-	+	+	-	+
	Search for homologous TFBS^#	-	-	-	-	+	-	+	-	-	-	-	+
3D Structure/Drug design	Visualization	-	-	+	-	-	-	-	-	-	-	+	+
	Ligand search	+	+	+	+	-	-	-	+	-	-	+	+
Back-end Database	General	+	+	+	+	+	-	+	+	+/-	+/-	+	+
	Integration of user's data	+	?	-	?	?	-	-	-	-	-	+	+
	Scalability	-	?	+	?	?	-	?	-	?	?	?	+
	OBO ontologies integration	-	-	-	-	-	-	-	-	-	-	-	+
General	Project Workspace, Data Sharing	+	+	-	+	+	-	+	+/-	+	+	+	+
	API/Plugins	+	+	-	+	+	+	-	+	+	+	+	+/-
	Free for Academic Use	-	-	+	-	-	+	-	+	+	+	-	+

IN, Ingenuity; GG, GeneGO suite; PS, Ariadne Genomics Pathway Studio; GE, Genomatix suite; ST, STRING; CS, Cytoscape; VS, VisANT; PA, Partek; PP, PipelinePilot; GX, Galaxy; TV, Taverna; BN, BiologicalNetworks.
+, a feature is present; -, not present; +/-, present but not fully; ?, unknown/cannot be determined;
#, TFBS, transcription factor binding site

ISSN: 1471-2105