PMC:1794230 / 33429-34894 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1794230","sourcedb":"PMC","sourceid":"1794230","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1794230","text":"PhyloScan evaluates significance at the level of the intergenic region\nA key focus of this work has been to combine evidence across transcription factor binding sites within an intergenic region and across orthologous regions in order to correctly identify intergenic regions that are likely to contain transcription factor binding sites, even when each of the identified transcription factor binding sites, considered in isolation, may not be sufficiently strong to be statistically significant. Accordingly, the individual sites included in our predictions are not necessarily statistically significant and individual site predictions may be false positives even within true-positive intergenic sequences.\nFor instance, in the collection of 10,000 synthetic data sets in which we planted two full-strength Crp transcription factor binding sites per intergenic region, we have 9,985 true positive intergenic regions at the 99.9% specificity level (see Figure 3). Of these true positives, in 6,287 of the E. coli intergenic regions two sites were predicted and the sites exactly coincided with the two planted sites. In 24 E. coli intergenic regions two sites were predicted and one of the two sites exactly coincided with a planted site. In 3,672 of these regions one site was predicted and it exactly coincided with one of the two planted sites, and in 2 of the E. coli intergenic regions, one site was predicted that did not exactly coincide with a planted site.","divisions":[{"label":"title","span":{"begin":0,"end":70}},{"label":"p","span":{"begin":71,"end":707}}],"tracks":[]}