Citation Context

...es for microRNA Binding Site Contextual Features. Supplementary Results Supplementary Methods Supplementary Figure 1: Flow chart illustrating the initial microRNA binding site identification steps. Supplementary Figure 1: Flow chart illustrating the initial microRNA binding site identification steps. As described in the Supplemental Results and Supplemental Methods sections, we began by running RNAhybrid using all C. elegans 3’ UTR and microRNA sequences as input. We then implemented several liberal filters to reduce noise. These included: (1) a threshold on the hybrid interaction energy, ΔG, (2) a limit on the G:U wobble pairs and bulges allowed within the seed region and (3) a conservation filter requiring that the above two filters be passed in orthologous C. elegans and C. briggsae 3’ UTRs. Details on these filters are given in the text of Supplemental Methods. The resulting list of binding sites formed the input for all of the subsequent analysis (see Figure 1). Supplementary Figure 2: Contextual Features Not Correlated with Enrichment for AIN-IP Transcripts. Fig 2 a Fig 2 b Fig 2 c Supplementary Figure 2: Contextual Features Not Correlated with Enrichment for AIN-IP Transcripts....

Citation Context

...ementary Table 2 Lists of Enrichment Values and P-values for microRNA Binding Site Contextual Features. Supplementary Results Supplementary Methods Supplementary Figure 1: Flow chart illustrating the initial microRNA binding site identification steps. Supplementary Figure 1: Flow chart illustrating the initial microRNA binding site identification steps. As described in the Supplemental Results and Supplemental Methods sections, we began by running RNAhybrid using all C. elegans 3’ UTR and microRNA sequences as input. We then implemented several liberal filters to reduce noise. These included: (1) a threshold on the hybrid interaction energy, ΔG, (2) a limit on the G:U wobble pairs and bulges allowed within the seed region and (3) a conservation filter requiring that the above two filters be passed in orthologous C. elegans and C. briggsae 3’ UTRs. Details on these filters are given in the text of Supplemental Methods. The resulting list of binding sites formed the input for all of the subsequent analysis (see Figure 1). Supplementary Figure 2: Contextual Features Not Correlated with Enrichment for AIN-IP Transcripts. Fig 2 a Fig 2 b Fig 2 c Supplementary Figure 2: Contextual Features ...

Citation Context

...Gtotal bins from -12 to -24 kcal/mol. Bins of ΔGtotal < -24 kcal/mol did not have enough counts to be statistically significant. Similarly, for structural availability, P-values were less than 0.05 for bins of 50-90% average open nucleotides in the upstream window. For the post-filter enrichments, which were derived from 100 random shuffles of the data, we calculated the P-values from the Z-score of a normal distribution. That is, random data shuffling should produce random noise in the calculated enrichments. We checked that this was true by first looking at a small number of random shuffles (10), observing that the standard deviations were relatively small (early convergence on the mean), then repeating the entire algorithm for a total of 100 iterations. The P-value for rejection of the null hypothesis (that the feature is not enriched) is the distance of each enrichment from the null hypothesis (relative enrichment – 1), divided by the standard deviation from the mean – in other words, a Z-score. Scoring microRNA Sites, Families and Targets Testing alternative modes of combining weights for different parameters Contributions from the three enriched features: seed topology (represent...

Citation Context

...ary Methods Supplementary Figure 1: Flow chart illustrating the initial microRNA binding site identification steps. Supplementary Figure 1: Flow chart illustrating the initial microRNA binding site identification steps. As described in the Supplemental Results and Supplemental Methods sections, we began by running RNAhybrid using all C. elegans 3’ UTR and microRNA sequences as input. We then implemented several liberal filters to reduce noise. These included: (1) a threshold on the hybrid interaction energy, ΔG, (2) a limit on the G:U wobble pairs and bulges allowed within the seed region and (3) a conservation filter requiring that the above two filters be passed in orthologous C. elegans and C. briggsae 3’ UTRs. Details on these filters are given in the text of Supplemental Methods. The resulting list of binding sites formed the input for all of the subsequent analysis (see Figure 1). Supplementary Figure 2: Contextual Features Not Correlated with Enrichment for AIN-IP Transcripts. Fig 2 a Fig 2 b Fig 2 c Supplementary Figure 2: Contextual Features Not Correlated with Enrichment for AIN-IP Transcripts. We evaluated several other features that have been proposed to correlate with eff...