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A Monte-Carlo assessment further confirmed that the enrichment of paired PPARγ/RXR binding sites is significant at FDR<0.05 when these bona fide individual binding sites are separated by <300 bp (Figure 3C).
The nature and distribution of the various receptor binding sites is significant in patterns of control.
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However, a model featuring the number of MTP binding sites is also a statistically significant predictor of the probability of a statistically significant call when oligo-dT alone is used (P = 0.02, slope 0.03).
Only 5% of STAT3 binding sites were deemed significant in transformed cells but not in non-transformed cells and also exhibit a greater than 5-fold increase in binding amplitude by ChIP-seq during transformation.
However, in these experiments we observed considerably higher background binding than in S2 cells, and, therefore, only 21 binding sites were statistically significant (false discovery rate (FDR) <10%), 19 of which overlap peaks in S2 cells.
The increased apparent dimerization constant imparted by adding a second equivalent binding site is of significant importance to development of allosteric regulators, and is expected to be present in the intact receptor as well as the LBD (see SI).
Five different protein models and active binding sites were predicted at significant cut-off confidence (C ≥ -1.5) and binding site (BS ≥ 0.5) scores.
Only half of the previously known MrpC binding sites were detected as significant peaks in both replicates of our ChIP-seq analysis (Table 2).
A binding p-value was then determined for each genomic position by Wilcoxon rank sum test and binding sites were generated from those more significant than specified thresholds with a maximum gap of 500 and minimum run of 350.
Transcription factor (TF) binding sites are then predicted by detecting statistically significant TF binding sequences on the genome using a position weight matrix.
Conversely, significant numbers of binding sites are located in regions far distant from the TSS or introns.
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