D.P. Zimmer, O. Paliy, B. Thomas, P. Gyaneshwar, and S. Kustu

Genome Image programs: visualization and interpretation of Escherichia coli microarray experiments (2004) Genetics, 167, 2111-2119.

Results of hierarchical clustering of a set of 11 experiments used in Zimmer et al [2000] to define the NtrC-Nac regulon of E. coli

• Agglomerative hierarchical clustering method was used (average linkage, centered Pearson correlation). The data blanks were filled by K-nearest neighbors algorithm (K=11) in SAM. Cluster and TreeView package were utilized to run and visualize the clustering.
• For experiment description (a-k), refer to Zimmer et al. 2000 Proc. Natl. Acad. Sci. USA 97:14674-14679.
• Only the 5 clusters that contained genes from the NtrC-Nac regulon are shown. NtrC-regulated genes are marked with a blue circle and nac-regulated genes are marked with a pink circle.