Computational protocol: Microarray analysis of Neosartorya fischeri using different carbon sources, petroleum asphaltenes and glucose-peptone

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Protocol publication

[…] Acquisition and quantification of array images were performed in GenePix 4100A with GenePix software by Molecular Devices. All images were captured using optimal laser power and 5 μm resolution. For each spot the Cy3 and Cy5 density mean value and the Cy3 and Cy5 background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.Microarray data analysis was performed using genArise software, developed by the Computing Unit of the Institute of Cellular Physiology of UNAM (http://www.ifc.unam.mx/genarise/). This software carry out background correction, Lowess normalization, intensity filter, analysis of replicates and selection of differentially expressed genes to identify those that show accurate evidence of differential expression by calculating an intensity-dependent z-score. It uses a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean.zi=Ri–meanR/sdRwhere zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.In order to perform functional annotation of the genes, sequences were aligned using the blast2go tool . […]

Pipeline specifications

Software tools genArise, Blast2GO
Application Gene expression microarray analysis
Organisms Aspergillus fischeri, Aspergillus fischeri NRRL 181
Chemicals Carbon, Glucose