Mapping of compact RNA clusters The mapping of tiny RNAs to lncRNA exons from lncRNAdb was carried out using bespoke script written in Perl. Only compact RNAs mapping completely to an lncRNA exons and mapping in the identical strand orienta tion were deemed for more evaluation. The expression information was retrieved for respective mapped clusters manu ally for comparison at tissue degree. We in addition per formed mappings making use of a comparable approach across the lncRNA exons and introns over the independent dataset of human lncRNA annotations from Gencode. An more than see of the computational analysis pipeline is described in Figure three. Reviewers remarks Reviewers Report Title, Integrative transcriptomes evaluation suggest proces sing of a subset of long non codingRNAs to small RNAs Versions, 1, two 3 9 January 2012 /12 April 2012/21 June 2012.
Reviewer Number, 1. Reviewer, Dr Rory Johnson. 1. Sample dimension, The authors carry out their analysis on an extremely limited set 72 of manually curated RNAs from lncrnadb. As a result, selleckchem results from this kind of a modest set provide us very tiny insight into whether or not this is a common phenomenon or not. Massive lncRNA annotations with a number of thousand examples in mouse or human happen to be out there for pretty some time. I’m baffled why the evaluation was not carried out working with such a set. Authors response, Our original analysis was initially carried out on a smaller dataset of 72 manually curated lncRNAs derived from lncRNAd, a publicly available database. This database includes examples of lncRNAs which have some level of biological perform assigned to them primarily based on literature proof.
This examination uncovered that thirty lncRNAs harbor 69 little RNA clusters as derived from clustering of little RNA sequencing selleck chemicals PHA-665752 reads, effects as depicted in More File two. We’ve now extended the examination employing a bigger dataset of manu ally curated 28,389 lncRNAs transcripts from Gencode edition ten. We followed the very similar methodology as depicted in Figure 3 to map the deepBase clusters onto the lncRNAs exonic areas. This added evaluation exposed a total of 1575 mappings in which 1259 lncRNAs exons harbor 1084 little RNA clusters. 2. Data presentation, The authors principle examination would be to compare the genomic coordinates of lncRNAs and tiny RNA clusters. This is not a especially challen ging analysis, while nonetheless vital. Even so, the authors tend not to make the results readily available in any use ful format. Table one exhibits the genomic coordinates on the lncRNAs in query, but no valuable data concerning the overlapping deepBase clusters. How are potential researchers supposed to validate or use this information without the need of the extremely most simple location details for the overlap ping clusters Authors response, We thank the reviewer for this suggestion.