TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

Table 1 A comparison of web tools dedicated to molecular interactions.

		MIR@NT@N	STRING^d	MotifMap^e	GeneMANIA	APID^f	InnateDB	InteractomeBrowser
	Physical protein protein interactions	-	+	+	+	+	+	+
	Computationally predicted TF targets^a	+	-	+	-	-	-	+
	Experimentally observed TF targets^b	-	-	-	-	-	-	+
Database content	Predicted miRNA targets	+	-	-	-	-	-	+
	Regulatory interactions from literature	-	+	-	-	-	-	+
	Biological pathways	-	+	-	+	-	-	-
	Inferred functional interactions^c	-	+	-	+	-	-	-
	Batch query	+	+	-	+	-	-	+
Build-in graph visualizer	add/remove/hide inter-actors and interactions	-	-	-	-	+	-	+
	Movable nodes	-	+	ND	+	+	+	+
	Compartment-based layout	-	-	-	-	-	+	+

The table provides an overview of the types of molecular interactions and of the functionalities offered by representative web tools previously published. Informations were obtained from latest articles describing the servers. The presence or absence of the corresponding features is denoted by + or - respectively.
^a Refers to bioinformatic prediction of TFBSs using PWMs.
^b Refers to results from large-scale experimental methods that profile the binding of TFs to DNA at the genome-wide level (e.g.; ChIP-Seq, ChIP-chip, ...).
^c Refers to computational methods that aggregate various informations (e.g.; expression, genomic distance, conservation) to infer functional interactions.
^d Search Tool for the Retrieval of Interacting Genes/Proteins
^e MotifMap visualizer was not available during our tests. Informations related to the visualizer were obtained from documentation.
^f Agile Protein Interaction DataAnalyzer

ISSN: 1471-2105