Error bars represents standard error of the mean; n = 3. DOI: http://dx.doi.org/10.7554/eLife.00178.017 When we examined Scn9a transcripts for NOVA binding in HITS-CLIP data, we found no 3′ UTR tag clusters.
Similarly to the PDZbase data, we found extensive binding overlap between the PDZs in terms of raw numbers although with a distribution that was mildly shifted towards even more binding overlap between PDZs (Fig. S5).
From our ChIP-chip data, we found that Hmt1-binding is enriched across the 5'-regions that are proximal or within the gene body of the nuclear-encoded tRNA genes.
In contrast to the soluble data, we found clearly measurable IgG2 binding, with a forward kinetic rate six-fold lower than that of IgG1 but with an equilibrium affinity only threefold lower.
Iteratively leveraging the promoter analysis data and the GIST and LMS gene expression data, we found 74 different transcription factor binding motifs that were enriched in at least 1 of the 100 resampled sets of differentially expressed genes.
Using publicly available data, we found a significant enrichment of PU.1 binding sites in the preleukemic hypermethylated genes, suggesting that shortage of PU.1 makes PU.1 binding sites in the DNA accessible for aberrant methylation.
Interestingly, in our data we found a Deeply shared human HNF4A singleton TF binding event spanning rs2279744.
In agreement with our proliferation, migration, and invasion data, we found that the downregulation of FXR inhibited NF- κB DNA-binding activity.
Of those 73 loci identified by Westwood et al.,[32] that did not overlap directly with our ChIP-chip data, we found that 54 are within one cytological band of at least one HSF binding site (data not shown).
From the available data, we find little evidence to relate poor metal-binding capacity to the formation of detergent-insoluble SOD1 aggregates.
