PMC:1794230 / 43545-45864 JSONTXT

{"project":"2_test","denotations":[{"id":"17244358-8014990-1689325","span":{"begin":198,"end":200},"obj":"8014990"},{"id":"17244358-8014990-1689326","span":{"begin":1633,"end":1635},"obj":"8014990"},{"id":"17244358-12136103-1689327","span":{"begin":2285,"end":2287},"obj":"12136103"}],"text":"Combining evidence across sites within an intergenic region\nPhyloScan combines information from multiple predictions via a weighted Bonferroni test in a manner similar to that of Neuwald and Green [40]. Specifically, for a user-supplied value k, which defaults to 2, and user-supplied weights (w1,..., wk), which default to (0.9, 0.1), PhyloScan conservatively computes an intergenic region's p-value as\nP intergenic = min ⁡ { 1 , p 1 w 1 , p 2 w 2 , ... , p k w k } MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=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@5AAD@\nwhere the weights (w1,..., wk) are nonnegative and sum to one, and pi is the probability that a randomly generated, intergenic sequence alignment of the same size would have its ith best site as good as or better than the ith best site in the intergenic sequence data under consideration. The calculation is conservative because the underlying events whose probabilities are (p1,..., pk) are not statistically disjoint [40].\nThus, an intergenic region with a strong site will make its presence known via a strong (i.e., low) value for the p1/w1 term, and an intergenic region that does not have a strong site, but that does have an ith best site that is surprisingly strong (given its rank as ith best), will be detected through a strong value for the pi/wi term. This enables us to detect both transcription factors that tend to bind strongly but in isolation and transcription factors that tend to bind multiply but weakly.\nAn alternate approach for combining the contributions of multiple binding sites, that of seeking the p-value of the sum of their log-likelihoods [41], is not employed by PhyloScan."}