Table 1.

Selected pathway/network analysis resource that can benefit Proteomics data analysis.

Name	Description	Link	Reference	Functional Info Using	Topological Info Using
GoMiner	Gene Ontology (GO) analysis for Omic data	http://discover.nci.nih.gov/gominer/	[38]	Single molecule	Non
KEGG	Kyoto Encyclopedia of Genes and Genomes	http://www.genome.jp/kegg/	[24]	Molecular pathway	Non
DAVID	The Database for Annotation, Visualization and Integrated Discovery	http://david.abcc.ncifcrf.gov/	[39]	Molecular pathway	Small-scale
PID	Pathway Interaction Database	http://pid.nci.nih.gov/	[27]	Cellular pathway	Non
HPD	Human Pathway Database	http://bio.informatics.iupui.edu/HPD	[29]	Cellular pathway	Small-scale
GESA	Gene Set Enrichment Analysis	http://www.broadinstitute.org/gsea/	[40]	Cellular pathway	Small-scale
IPA	Ingenuity pathway analysis	http://www.ingenuity.com/	N/A	Molecular pathway	Small-scale
MetaCore	Thomson Reuters pathway analysis and knowledge mining	http://thomsonreuters.com/metacore/	N/A	Cellular pathway	Small-scale
Pathway-Express	A systems biology approach for pathway level impact analysis	http://vortex.cs.wayne.edu/projects.htm	[36]	Molecular pathway	Mid-Scale
SPIA	Signaling Pathway Impact Analysis	http://www.bioconductor.org/packages/2.12/bioc/html/SPIA.html	[47]	Molecular pathway	Mid-Scale
PAGED	An integrated Pathway And Gene Enrichment Database	http://bio.informatics.iupui.edu/PAGED	[30]	System pathway	Mid-Scale
HAPPI	Human Annotated and Predicted Protein Interaction database	http://bio.informatics.iupui.edu/HAPPI	[28]	Single molecule	Large-scale
STRING	Search Tool for the Retrieval of Interacting Genes/Proteins	http://string.embl.de/	[23]	Single molecule	Large-scale
CytoScape	An open source platform for complex network analysis and visualization	http://www.cytoscape.org/	[46]	Molecular pathway	Large-scale
ACOR	Ant Colony Optimization Reordering	N/A	[67-70]	Molecular pathway	Large-scale
Gene-Terrain	Terrain-based visual analysis for complex networks	N/A	[79], [80]	Network module	Large-scale