Table 2 Summary of functional and network tools

Kyoto Encyclopedia of Genes and Genomes

http://www.genome.jp/kegg/

Kanehisa and Goto (2000) [76]

Pathway

The Database for Annotation, Visualization and Integrated Discovery

http://david.abcc.ncifcrf.gov/

Dennis et al. (2003) [96]

Pathway and functional annotation using GO

Pathway Interaction Database

http://pid.nci.nih.gov/

Schaefer et al. (2009) [97]

Pathway interaction

Ingenuity Pathway Analysis

http://www.ingenuity.com/

Pathway and functional annotation

An open source platform for complex network analysis and visualization

http://www.cytoscape.org/

Shannon et al. (2003) [98]

Network visualization

Human Annotated and Predicted Protein Interaction Database

http://bio.informatics.iupui.edu/HAPPI

Chen et al. (2009) [99]

Protein interaction

Gene Set Enrichment Analysis

http://www.broadinstitute.org/gsea/

Subramanian et al. (2005) [77]

Pathway analysis and functional annotation

Curated database of pathways and reactions (pathway steps)

http://www.reactome.org/

Matthews et al. (2009) [100]

Pathway

Pathway database

http://www.biocarta.com/

Nishimura (2001) [101]

Pathway

Integrated Human Pathway Database

http://discovery.informatics.iupui.edu/HPD/

Chowbina et al. (2009) [102]

Pathway

Pathway and Gene Enrichment Database

http://omictools.com/paged-s3492.html

Huang et al. (2012) [103]

Pathway, functional annotation

Human Protein Reference Database

http://www.hprd.org/

Keshava Prasad, T. S. et al. (2009) [104]

Annotation

Drug Bank

http://www.drugbank.ca/

Combines drug data with drug target

Consensus Path DB

http://consensuspathdb.org/

Kamburov, A. et al. (2013) [105]

Interaction networks (protein-protein, genetic, metabolic, signaling, gene regulatory, and drug-target)

Biological Network Gene Ontology Tool

http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

Maere S, Heymans K, and Kuiper M (2005) [106]

Biological network gene ontology

Gene Annotation Tool to Help Explain Relationships

http://gather.genome.duke.edu

Chang JT, and Nevins JR. (2006) [84]

Gene annotation tool