As advised from the reviewer Table one, now Extra File 2 has become modified with include itional facts to provide researchers having a ready set of reference to potentially prioritize them for additional experiments. We have incorporated two additional columns in Added File 2 i. e. Cluster destinations and Strand additionally towards the existing columns lncRNA Name, Genomic Place, Length of lncRNA and deepBase Clusters. 3. Information validation, Yet another main issue with this particular evaluation is that the authors make totally no energy to know whether or not the overlaps that they observe be tween lncRNAs and smaller RNA clusters is any distinct from everything you expect by opportunity. There are plenty of ana lyses that come to mind to see whether the observed overlap is specifically higher or not.
It’s important to cal culate the real overlap price, and many unfavorable and beneficial management overlap costs, and calculate a resulting selleck inhibitor P value for your distinctions. The authors never even men tion whether or not the small RNA clusters originate to the similar or opposite strand in the supposed host lncRNA transcript this is certainly crucial, I cannot come across it pointed out while in the Resources and Approaches. Other critical concerns, do the little RNAs originate from introns or exons of lncRNAs Do tiny RNA clusters overlap protein coding genes with the exact same rate as lncRNAs One more valuable con trol evaluation will be to exclusively select lncRNAs that are acknowledged to become tiny RNA precursors and determine the price of overlap right here, being a comparison.
Authors response, We thank the reviewers for that sug gestion, although we tend not to subscribe for the assumption that the smallRNAs mapping to lncRNAs must be sig nificantly kinase inhibitor TSA hdac inhibitor enriched to assume processing or biological functionality. We now have indeed in contrast the mapping frequencies to exons and introns in protein coding also as lengthy non coding genes. Examination exposed 1575 modest RNA deepBase cluster mapped onto lncRNA exons using a length adjusted frequency of 0. 093 per kilobase though clusters mapped that has a frequency of 0. 042 per kilobase towards the introns. A related analysis of protein coding genes unveiled a length adjusted frequency of 0. 29 per kilobase for exons and 0. 059 per kilobase for introns. We thank the reviewer for pointing out the Mate rials section did not incorporate adequate information and facts on the strand/orientation on the transcript and smallRNA clus ters.
The tiny RNA clusters which overlap host lncRNA were mapped keeping into consideration the strand as depicted in More File 2 and Additional File 3. The Materials and Procedures part of your manuscript also has become modified accordingly. So far as I can see the data in Added File two has a minimum of two critical mistakes, which lead me to doubt the excellent of this dataset, one BC200 is usually a human repeat component, with numerous cop ies through the entire genome.