This article is one of a series of three by us discussing the interpretation of gene function using networks. We summarize and unify the arguments made in those articles in an opinion piece:

http://f1000research.com/...

The original articles may be found at:

Gillis J., Pavlidis P. (2011) "The impact of multifunctional genes on "guilt by association" analysis." PLoS ONE 6(2):e17258.
http://www.plosone.org/ar...

Gillis J., Pavlidis P. (2011) "The role of indirect connections in gene networks in predicting function." Bioinformatics 27(13):1860-6.
http://bioinformatics.oxf...

Gillis J, Pavlidis P (2012) “'Guilt by Association' Is the Exception Rather Than the Rule in Gene Networks." PLoS Comput Biol 8(3): e1002444.
http://www.ploscompbiol.o...