In addition, we examined how many genes bound by σ in the WT strain were bound by σ when rpoS was deleted.
Reviewer 2 raised a point about whether target genes that were repressed and bound by Hairy in vivo were in fact direct functional targets of the protein, since some repressed genes were not bound by Hairy, and many genes bound by Hairy are not repressed (consistent with our findings that Hairy has many nonfunctional sites).
The distribution of genes and regulatory modules reveal that many genes are bound by multiple TFs.
This would be very helpful as it would make it obvious how many genes are, as the Hox genes, bound in all 3 conditions, how many are, as Skap2 (arrow in Figure 5D), bound by Crm1 only in the presence of Nup98-HoxA9.
Further functional annotation of c-Myc targets using IPA identified many additional cell cycle regulatory genes bound by c-Myc such as Bard1, Bax, Ctcf, Daxx, Dnmt1, Hes1, Max, Mycn, Rb1, and Sox2.
Here we found that several genes involved in processes other than protein folding (mainly in RNA processing and DNA replication, recombination and repair) were bound by HSF1, and that many genes were similarly bound by HSF1 in both hepatocytes and spermatocytes despite a completely different nature in the resulting transcriptional response.
Many genes known to bind these transcription factors and form part of the extended transcriptional network influencing pluripotency of ES cells were also found to be downregulated [32], [33].
Although the most significantly enriched class of target genes encode transcription factors, we find that Ubx is bound to many genes that carry out a wide variety of functions.
STAT3 also binds near many genes that are up-regulated in ABC cells relative to GCB cells; these genes have a wide range of functions that are pertinent to oncogenesis, especially apoptosis and cellular signaling.
It is known that NFI occupies the promoters of many genes where it may bind synergistically with some other transcription factors such as hepatocyte nuclear factor 1 alpha, estrogen receptor, Brg-associated factor [ 31- 33].
Although, many strongly bound genes are close to a high affinity site neither our promoter motif nor our coding sequence signatures show any correlation to HAS.
