RNAcompete

[…] lt, we got an average PCC = 0.417 which was much closer to DeepBind (no statistically significant difference) and RCK (still significantly stronger), with much less training time. When trained on one RNAcompete experiment (using set A only) on the same machine, KNN-RCK took < 1 hr (53min on average over a subset of 14 experiments); RCK took 3–4 hrs (220min on average), both with the hyper-paramete […]

[…] We explored the overall statistic of structural binding preferences amongst the set of RNA-binding proteins in the RNAcompete dataset []. We used the set of learned models from the RCK website []. We identified for each protein the k-mer w and structural context a with the highest binding score. We calculated the […]

[…] between direct and indirect splicing regulation–we consider that any AS event that is affected by a SF but that has no consensus binding site is indirectly affected by that SF. We previously used the RNAcompete method [,] to define the in vitro binding specificities of our SFs of interest. We were able to obtain 7-mer binding motifs for each SF, reproducing both known [,,] as well as novel consens […]

[…] understand whether the motifs deduced for RBM10 in vivo targets related to intrinsic sequence specificity of this protein, we analyzed the binding preference of its main RNA interacting region using RNAcompete (,) (Figure ). Briefly, purified proteins were incubated with a 75-fold excess of a non-randomized RNA pool, RBM10-selected RNAs were identified using microarray analysis and RNA-binding pr […]

[…] eferred as binding motifs. Detecting them can facilitate the deeper insights into post-transcriptional regulation.Although there are many genome-wide RNA-binding protein detection techniques, such as RNAcompete [], PAR-CLIP [], they are still cost-heavy and time-intensive. Fortunately, with the advent of these high-throughput techniques, many useful genome-wide data associated with RBPs are genera […]

[…] tary information to protein RNA-binding preferences.Toward this aim, high-throughput in vitro methods have been developed to study the binding preferences of RBPs (Ray et al., ; Lambert et al., ). In RNAcompete (Ray et al., ), a specific protein binds to a set of predesigned oligos, and binding is measured using a florescence tag. The binding of the protein to a set of more than 200,000 probe sequ […]