Ults in Additional File 4 and also added these results in the
Ults in Additional File 4 and also added these results in the revised manuscript. 8. Table 1, Figure 2, Figure 3 ?the data is presented with little useful detail (eg Table 1 ?what are the Cluster locations and strand?, Figure 2, what are theactualnumbers of RNAs, not ages?) and the Figure Legends are way to short and lacking also useful details. Author’s response: As suggested by the reviewer Table 1 (Additional File 2 in revised manuscript) has been modified and 2 additional columns are added i.e. Cluster locations and purchase AZD4547 strand in addition to the existing columns “lncRNA Name”, “Genomic Position”, “Length of PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27107493 lncRNA” and “deepBase Clusters”. We hope this would serve as a ready reference and starting point for experimental validation of interesting candidates. We have also revised the figure legends with more details as suggested. 9. Supplementary Figure 3 seems to be identical to main Figure 3. Author’s response: In revised manuscript, the Supplementary Figure 3, is placed as Additional File 6 and Figure 3, is now Figure 1. 10. In general, I do not find the Supplementary Files particularly useful or relevant to the paper. Author’s response: The Supplementary Files have been modified in the revised manuscript. We have only included Tables and Figures relevant to the paper and removed the redundant ones. I thank the Authors for responding comprehensively to my comments. I continue to have doubts about the value of this paper. I have the impression that the analysis and manuscript preparation has been carried in a rather careless way, without consideration of the implications of the work, or for with clarity for the reader. Furthermore, I am concerned by the lack of clarity from the Authors about whether the claimed small RNA overlaps are occurring on the same strand as the claimed host lncRNA – an issue of crucial importance to this manuscript. Author’s response: We have analyzed the smallRNA clusters as annotated by DeepBase and falling in the same orientation as the lncRNA. The manuscript section has been modified appropriately to detail the analysis methodology. We agree with the reviewer that the computational analysis does not provide much insight into the potential biological implications of the observation. In fact, in present situation, our understanding of biological functions for majority of lncRNAs is not known and computational methods to functionally assign roles are still na e. The present report serves as a starting point and ready reference to a dataset which suggests that a subset of lncRNAs could potentially be processed to smaller RNAs. In the revised manuscript, we detail our observation on a relatively well studied lncRNA. The lncRNA PTENTP1 is a pseudogene of PTEN gene. Our analysis reveals that PTENP1 harbors 5 small RNAs clusters as annotated by deepBase. This observation is also corroborated by independent dataset of small RNA cloning data fromJalali et al. Biology Direct 2012, 7:25 http://www.biology-direct.com/content/7/1/Page 9 ofsmiRNAdb [33] which revealed that the fifth cluster comprises of three distinct small RNA clusters, having differential expression levels in different tissues as depicted in Figure1. This could lead to a possibility whereby apart from the PTENP1 function; the processed small RNAs could be an additional mechanism for modulating biological processes in the cell and potentially in the pathogenesis of oncogenesis. We have compiled our results in tabular format which is available along with.