Computational protocol: Transcriptional Profiling of Bacillus anthracis Sterne (34F2) during Iron Starvation

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Protocol publication

[…] Analysis of the microarray data was carried out using Gene Expression Data Analyzer (GEDA; http://bioinformatics.upmc.edu/GE2/GEDA.html) . Briefly, this online software package was used for statistical comparisons of individual conditions at each timepoint. Data were grouped into categories, IDM or IRM, and subjected to the J5 statistical analysis, which is designed for data sets with limited numbers of replicates and reduces the chances of false positives . Genes were considered statistically significant if they had a J5 score greater than 2 and exhibited a fold change greater than 2. Supplementary and report both the J5 value and fold change for genes that changed significantly at each timepoint. Genes meeting these requirements were then entered into GenePattern and data are presented as a hierarchical clustering (Pearson correlation) of log2 transformed normalized intensity values for these genes. Our datasets have been deposited to the ArrayExpress database under the accession number E-MEXP-2272. […]

Pipeline specifications

Software tools GEDA, GenePattern
Databases ArrayExpress
Application Gene expression microarray analysis
Organisms Mus musculus, Bacillus anthracis, Bacillus anthracis str. Sterne
Diseases Infection
Chemicals Iron