First we searched for well-expressed genes (>3 FPKM) with a flat expression profile over the set of all available brain regions.
Last week, President Obama became the latest to fail to put on what people in the television business call "neutral face," a warm but flat expression that betrays no hint of whatever feelings might be simmering inside.
She leaned up against her bike with a flat expression on her face.
The MdP was distinguished by a dramatic increase in the expression levels of Thbs4 (GeneID: 21828) compared with the other prominences, but relatively flat expression of Sdc2 (GeneID: 15529).
The resulting PIRS was minimized for genes that exhibit both flat expression as a function of time and low variance in observed expression at each time point.
On average, tissue-specific genes (τ ≈ 1) had about equal expression in males and females, whereas genes with close to flat expression profiles showed about two times higher expression in males than in females (fig. 1).
In all cases, the genes selected by our metric show flat expression with low variation, whereas genes that rank poorly show high variation both within and between time points (compare Figure 1, Figure 2, and Figure 3 to Figure S4).
Details, including compliance with MIQE guidelines [ 14], are available in Additional files 2 and 3. Flat expression patterns across samples in the derivation dataset were filtered out by excluding genes with standard deviations ≤ 0.1.
Furthermore, genes with flat expression profiles might also have little representation in the network; only 14 out of the 100 genes with most steady expression profiles were incorporated into a cluster, while 68 were filtered out due to low similarity to any other gene.
Second, in this S. cerevisiae dataset, it is known that the genes coding for key regulators of the stress response system, i.e. transcription factors Yap1, Pdr1 and Pdr3, exhibit flat expression patterns during stress condition (Additional file 4); this prevents the use of correlation measures with their expression profiles to identify causal relationships with their potential target genes.
