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Expression intensities of differentially expressed hematological genes were used in cluster analyses.
The expression intensities of the molecular layer remain largely constant and due to the low number of cell bodies the expression intensities of the different probes vary widely.
The distributions of expression intensities conferred by P1 and P2 promoters are similar (Figure S2).
The highest relative expression intensities were found between E17.5 and P1.
A Loess transformation was performed using Beehive (http://stagbeetle.animal.uiuc.edu/Beehive) to normalize expression intensities.
This method has the advantage that it makes no assumptions about the distribution of expression intensities.
Expression intensities of 98 and 138 genes were extracted from the upregulated and downregulated genesets, respectively.
Note that a threshold of 1.5 in Log2 Ratios is equivalent to almost a three fold change in expression intensities.
This procedure yields identical distributions of overall expression intensities across treatments, even if they were very different to begin with.
Genes were then clustered on the basis of their normalized expression intensities using the Avadis software (version 3.1, Stratagene).
Reporters with expression intensities of less than 10% of the array median were removed from the dataset.
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