Table 2.

Web servers providing the analyses of biological pathways

Number	Web server	Objective	Data Input	URL	Reference
1	GeneNetwork	Inferring genetic network architecture from microarray data	Gene expression data	http://genenetwork.sbl.bc.sinica	[122]
2	MetaReg	Modeling and analysis of a biological network from high throughput data	Gene expression data	http://acgt.cs.tau.ac.il/metareg/application.html	[123]
3	WGCNA	Identifying clusters (modules) of highly correlated genes	Gene expression data	http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/	[124]
4	YEASTRACT-DISCOVERER	Identifying and visualizing transcription regulatory networks and associations between TF and target genes	Gene expression data	http://www.yeastract.com/	[125]
5	GeneNT	Network constrained (NC) clustering	Gene expression data	http://crantastic.org/packages/GeneNT	[122]
6	NetworkAnalyst	Network analysis and visualization by mining gene expression data	Gene expression data	http://www.networkanalyst.ca/NetworkAnalyst/	[126]
7	KEGGanim	Visualize the gene expression data in KEGG pathways	Gene expression data	http://biit.cs.ut.ee/kegganim/	[127]
8	ASIAN	Infer a framework of regulatory networks from gene expression data.	Gene expression data	http://www.mrc-lmb.cam.ac.uk/genomes/madanm/blang/methods/AburataniS.ASIAN.awebserver forinferringa.html	[128]
9	ArrayXPath	Visualize gene-expression data in integrated biological pathway	Gene expression data	http://www.snubi.org/software/ArrayXPath/	[129]
10	VisHiC	Cluster and interpret gene expression microarray data	Gene expression data	http://www.hsls.pitt.edu/obrc/index.php?page=gene_expression_tools	[130]
11	PANA	Integrate the functional annotation with gene expression data to discover functional relationship among pathways	Functional annotation data, Gene expression data	http://cs.uns.edu.ar/∼ip/PANA/	[60]
12	NetSearch	Identifying signaling pathways from microarray expression data and protein interactions	Gene expression data, Protein–protein interaction	http://arep.med.harvard.edu/NetSearch/runprog.html	[24]
13	Struct2net	Protein–protein interaction detection based on structural information with functional annotation	Protein–protein interaction data, Protein sequence	http://groups.csail.mit.edu/cb/struct2net/webserver/	[131, 132]
14	GraphWeb	Mine large biological networks for smaller modules, discover novel candidates and connections for known pathways	Protein–protein interaction data, Directed regulatory data	http://biit.cs.ut.ee/graphweb/	[133]
15	NeAT	Analysis of biological networks/pathway, including path finding, network clustering, etc.	Functional annotation data, Gene expression data, protein interaction data	http://rsat.ulb.ac.be/rsat/index_neat.html	[134]
16	KOBAS server	Annotate protein sequences with KEGG Orthology terms and identify significantly enriched pathways	Protein sequence data	http://kobas.cbi.pku.edu.cn/home.do	[135]
17	PHT-Pathway Hunter Tool	Perform shortest path analysis in the metabolic pathway	Substrate and product metabolite of a reaction in the pathway	http://pht.tu-bs.de/	[136]