Sentence examples for binding sites were ranked from inspiring English sources
To reduce the complexity associated with carrying forward multiple cavities per protein for BSC, the detected binding sites were ranked and subsequently filtered according to their potential to bind a small molecule ligand.
EIN3 binding sites were ranked using the R package timecourse, which has been previously used to analyze microarray timecourse data.
Predicted binding sites were ranked according to their free energy and we report the highest ranking prediction that overlaps an annotated binding site in Table 2, as it has been done by Tafer and Hofacker (2008).
We next examined the ranked sum expression of these targets and determined that transcripts with Ago2 HITS-CLIP miR-203 binding sites were ranked significantly higher compared to non-targeted mRNAs, indicating that many of these targets are functional.
Lists of target binding sites are ranked first by p-value from most significant to least significant and in second by the difference between the ChIP DNA and input DNA read counts from the highest to the lowest.
The presumed SSZ-binding sites were ranked by conservation score, specifically by the frequency of occurrence of a residue in a contact surface.
Briefly, each of the 978 ATP-binding sites are ranked by decreasing distance to that of synapsin I and the rank distribution of every binding site sharing the same protein name (true positives are presumed similar to the reference) are compared to the ranks of all other active sites (true negatives are presumed dissimilar to the reference, see full results in Supplementary Table S2).
All sites were ranked by t-value and input into GSEA as a ranked list.
Sites are ranked by latitude (north to south).
Enriched transcription factor binding sites were then ranked by the differences between the expected values for the divergent gene set and the set of all RefSeq promoters (Table 2).
The most popular of these sites is ZDNet, ranked 17th by Media Metrix, while Time Warner's Pathfinder site is ranked 27th.
