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Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles

Richard D Waite1*, Alberto Paccanaro12, Anastasia Papakonstantinopoulou1, Jacob M Hurst1, Mansoor Saqi1, Eddie Littler3 and Michael A Curtis1

Author Affiliations

1 MRC Molecular Pathogenesis Research Unit, Centre for Infectious Disease, Institute of Cell and Molecular Science, Barts and the London, Queen Mary School of Medicine and Dentistry, 4 Newark Street, London, E1 2AT, UK

2 Department of Computer Science, Royal Holloway, University of London Egham, TW20 0EX, UK

3 Medivir UK Ltd, Peterhouse Technology Park, 100 Fulbourn Road, Cambridge CB1 9PT, UK

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BMC Genomics 2006, 7:162  doi:10.1186/1471-2164-7-162

Published: 26 June 2006

Additional files

Additional file 1:

Figure S1. Results of clustering the expression data with K-means spectral clustering (K = 10) and hierarchical clustering with ward linkage. Shows the expression profiles obtained through these two methods of clustering. It also compares these two clustering methods with K-means clustering (K = 10) which is shown in the paper. For this analysis the average of replicates for each condition was used. Figure S2. Functional class representation in the ten clusters created by K-means clustering. From this figure it can be determined what percentage of genes in each of twenty-six functional classes are present in each cluster. Figure S3. Results of K-means clustering (K = 10) of expression data from all replicates from all six conditions. Shows an Eisen diagram of the expression profiles grouped according to the results of the clustering and a graphical plot of the profiles in each cluster.

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Additional file 2:

Table S1. Contains a list of all genes that display low expression in all six conditions studied. This list contains genes showing very low expression (under 50 signal units for all three replicates) for all six different conditions. These 1429 genes were not used in the clustering analysis. The table displays the average microarray expression results for each gene for each condition. Table S2. Contains a list of genes in which gene expression did not vary significantly between the six different conditions. This list was obtained using a 1-way ANOVA (assuming unequal variances) and genes in this list were not used in the clustering analysis. The table displays the average microarray expression results for each gene for each condition.

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Additional file 3:

Tables S3 – S12. Genes present in the clusters obtained by K-means clustering (K = 10). The genes in clusters 1 -10 are displayed together with their average microarray expression results for each condition.

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