Data Quantification: For visual assessment and quantification of microarray data, TIFF images are downloaded in software Imagene 6.0. Every spot is quantified by pixel intensity measurement. The following parameters are taken into account:

• low signal to noise ratio
• data is in linear dynamic range
• a background of 200-500 is seen for cy3 and 500-800 for cy5
• an absent flag is applied if spots contain no DNA in both channels
• a negative flag is applied if background intensity is more than signal
• auto segmentation is activated (this is a proprietary algorithm developed by Biodiscovery that allows the user to preview each spot for the assessment of signal and background in both channels). It is highly recommended to see the quality of spot, treatment of irregularities, spot shifting, printing irregularities, and dust/ humidity/ artifacts or bright spot of just dye
• a correlation between mean and median of pixel intensities as measure for spot quality is determined
• flagged spots are not included for further analysis but related genes can be recovered by further analysis. Quantified data is placed in text files and is ready for further analysis