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Fig. 1 Distribution of alternative splice forms for primary transcripts for which the most highly expressed transcript shows at least a twofold change in expression in light vs. dark conditions.

Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence.

In mice, there are six imprinted transcripts for which cDNAs have been cloned.

We found 22 Hox transcripts for which introns seem to encompass other genes.

The off-target signature is composed of transcripts for which (tgfup ∧ wotgfup) ∨ (tgfdown ∧ wotgfdown) ∨ (tgfup ∧ wotgfdown) ∨ (tgfdown ∧ wotgfup).

It is also only of use for the most abundant transcripts (for which contigs could be created).

Of particular note were increases in the apoliprotein L (APOL) transcripts, for which the increased expression of APOL2 was validated by QPCR ( Fig. 3 ).

This fraction also contains transcripts for which microarray probes are not performing as intended, which further reduces the number of potentially silent genes almost to none.

Three additional transcripts, for which corresponding EST sequences were identified in the S. gregaria database, were also evaluated as (putative) positive controls in this study (Table 5).

Transcripts for which expression was decreased were mainly associated with synaptic vesicular trafficking, clathrin-independent endocytosis or transport from the late endosome to the lysosome.

That fact, that we discovered only one motif in this work can be easily explained by the relatively small set of transcripts for which experimental data was available and which was used to derive a valid motif.

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