A coherent feed-forward loop with SUM input function prolongs flagella expression in Exherichia coli http://www.nature.com/msb/journal/v1/n1/full/msb4100010.html
Presents a complet analysis for a particular network motif. It is not a key paper for this topic but one that can be worth reading, expecially as an introduction
A global view of pleiotropy and phenotipically derived gene function in yeast http://www.nature.com/msb/journal/v1/n1/full/msb4100004.html
Relation between phenotypes and gene functions through essentially bi-clustering