Tool	Web-based Resource	Advantages	Limitations	Examples of Use
Gene Ontology (GO)	www.geneontology.org	Plentiful easy to use web resources Well-documented acceptance by scientific community	No standardization as to level of granularity of data presented Plastic gene assignments and terms	Normal urinary proteome [51] Glomerular proteome [44] Total Renal Proteome [107]
Pathway Analysis	www.genome.jp/kegg/	Static pathways (relative to other tools) Easy to conceptualize	Fails to account for inter-pathway interaction	TGFβ signaling in diabetic nephropathy [56]
Network Analysis	www.ingenuity.com www.genego.com www.cytoscape.org	Identifies inter-pathway interactions Not dependent on predefined abstractions of biological processes Allows integration of numerous biomolecules in systems biology	Difficult to quantify comparisons between experiments Networks depend on knowledge base of interactions (that is, there is not a standard knowledge base) Some disagreement as to interpretation of findings	Metabolomeproteome interactions involving retinoic acid in diabetic nephropathy [111] Plasma apolipoproteins in clinical diabetic nephropathy [112]