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(Noise) Let C 1,…, C k be the clusters of database D w.r.t.
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Because the fix involves making a query to a cluster of databases, that cluster was quickly overwhelmed by hundreds of thousands of queries a second.
Tables 1 and 2 describe two clusters of the database.
The KO database stores the list of orthologous genes (available at http://www.genome.jp/kegg/ko.html); thus, it is similar to the Clusters of Orthologous Group COGG) database [ 48].
MADMuscle statistically assesses the overlap between the input gene list and the lists relative to all the clusters of the database (see Additional File 2).
We show how the user can browse the microarray data related to muscle studies, examine the annotated clusters and compare his own gene list with the gene lists relative to all the clusters of the database.
The protein functional categories were obtained by protein BLAST searches to the Clusters of Orthologous Group COGG) database using an E-value cut-off of 0.001 and composition-corrected scoring approach [ 92, 93].
Each of the 1,247 "good" labeled clusters of the database was systematically compared to all others using the Fischer exact test to detect significant similarity (strong overlap) or dissimilarity (poor or no overlap).
Finally, to assess the differences between these two complete gene lists (+/+ and -/-), we analyzed their expression patterns, given by the 1,247 "good" labeled clusters of the database, with a Multidimensional scaling (MDS) [ 83].
Web applications can spike suddenly in demand or grow so big that they tax traditional databases, or even clusters of traditional databases, which are hard to maintain, especially for smaller companies.
Users can perform hierarchical, binning or multidimensional clustering analysis of database compounds using this tool.
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