This pro portion represents the FDR for that gPAR CLIP crosslinking site. Using a strict 1% FDR threshold, we identify 80,883 gPAR CLIP crosslinking sites. Effect of counting Veliparib purchase statistics on error in crosslinking site coverage measurement Read coverage of replicate gPAR CLIP crosslinking sites was analyzed to measure reproducibility. For each site, we compared Inhibitors,Modulators,Libraries the number of reads coming from one replicate library to the total number of reads from both libraries. Perfect reproducibility would result in a ratio of 1 2. We binned crosslinking sites based on total RPM and calculated the standard deviation of these ratios for each bin. We predicted the standard deviation for counting statistics by binomial partitioning of total reads for each crosslinking site in each bin between the two replicates.

When the total number of reads was below 5 RPM, binomial partitioning predominantly contributed to replicate variation. Above 5 RPM, replicate variation stabilized, and counting statistics error contributed little to replicate error. Conservation analysis phastCons conservation scores for each genomic nucleo tide were downloaded Inhibitors,Modulators,Libraries from Siepel et al. Ts with CLSs were grouped into 5 UTR, CDS, and 3 UTR regions and then ranked and Inhibitors,Modulators,Libraries binned by CLS so each bin overlapped adjacent bins by 50%. phastCons scores in each bin were averaged. As controls, Ts with no CLS were grouped in 5 UTR, CDS, and 3 UTR regions, ran domly ranked, and binned as described. Inhibitors,Modulators,Libraries phastCons scores in each bin were averaged. Controls were calcu lated ten times for each region.

Unpaired probability analysis The unpaired probability of each genomic position was calculated using RNAplfold from the ViennaRNA package version 1. 8. 5 using a span of 40 nucleotides and an averaging window of 80 nucleotides. Ts with CLSs were grouped into 5 UTR, CDS, and 3 UTR regions and then Inhibitors,Modulators,Libraries ranked and binned by CLS so each bin over lapped adjacent bins by 50%. Unpaired probabilities in each bin were averaged. As controls, Ts with no CLS were grouped into 5 UTR, CDS, and 3 UTR regions, randomly ranked, and binned. The unpaired probabil ities in each bin were averaged. Crosslinking site pairedness analysis Genomic regions corresponding to crosslinking sites were extended to 80 nucleotides http://www.selleckchem.com/products/CAL-101.html centered on the origi nal crosslinking site. These sequences were subjected to folding using RNAfold from the ViennaRNA pack age version 1. 8. 5, and the minimum free energy struc tures were extracted. Predicted structures were aligned and ranked by average crosslinking site CLS and divided into 100 equally sized, non overlapping bins. The per centage of nucleotides predicted to be unpaired at each position in each bin was computed. Selected structures from low, middle, and high CLS bins were visualized using VARNA.