Genome evolution reveals biochemical networks and functional modules

Christian von Mering, Evgeny M. Zodbnov, Sophia Tsoka, Francesca D. Ciccarelli, Jose B. Pereira-Leal, Christos A. Ouzounis & Peer Bork

European Molecular Biology Laboratory, D-69117 Heidelberg, Meyerhofstrasse 1, Germany Max-Delbrueck-Center for Molecular Medicine, D-13012 Berlin, Rober-Roessle-Str. 10, Germany Computational Genomics Group, European Bioinformatics Institute, Cambridge CB10 1SD, UK

Supplementary Online Data   [Supplementary Online Text]

The following are sets of predicted functional modules in Escherichia coli K12 - using a variety of clustering techniques and clustering parameters.   The set marked in red is the one chosen for detailed analysis in the paper.

UPGMA mean clustering Single Linkage Markov Clustering score cutoff 100: module list score cutoff 100: module list inflation parameter 1.5: module list score cutoff 200: module list score cutoff 200: module list inflation parameter 1.7: module list score cutoff 300: module list score cutoff 300: module list inflation parameter 2.0: module list score cutoff 350: module list score cutoff 350: module list inflation parameter 2.3: module list score cutoff 400: module list score cutoff 400: module list inflation parameter 2.5: module list score cutoff 450: module list score cutoff 450: module list inflation parameter 2.7: module list score cutoff 500: module list score cutoff 500: module list inflation parameter 3.0: module list score cutoff 600: module list score cutoff 600: module list inflation parameter 3.2: module list score cutoff 700: module list score cutoff 700: module list inflation parameter 3.5: module list