Abstract
MicroRNAs constitute a class of noncoding small RNAs involved in the posttranscriptional regulation of many biological pathways. In recent years, microRNAs have also been associated with regulation across kingdoms, demonstrating that exogenous miRNAs can function in mammals in a fashion similar to mammalian miRNAs. The growing interest in microRNAs and the increasing amount of literature and molecular and biomedical data available make it difficult to identify records of interest and keep up to date with novel findings. For these reasons, we developed the microRNA Analysis Portal (MAP). MAP selects relevant miRNA-focused articles from PubMed, links biomedical and molecular data and applies bioinformatics modules. At the time of this writing, MAP represents the richest, most complete and integrated database focused on microRNAs. MAP also integrates an updated version of MirCompare (2.0), a computational platform used for selecting plant microRNAs on the basis of their ability to regulate mammalian genes. Both MAP and MirCompare functionalities were used to predict that microRNAs from Moringa oleifera have putative roles across kingdoms by regulating human genes coding for proteins of the immune system. Starting from a selection of 94 human microRNAs, MirCompare selected 6 Moringa oleifera functional homologs. The subsequent prediction of human targets and areas of functional enrichment highlighted the central involvement of these genes in regulating immune system processes, particularly the host-virus interaction processes in hepatitis B, cytomegalovirus, papillomavirus and coronavirus. This case of use showed how MAP can help to perform complex queries without any computational background. MAP is available at http://stablab.uniroma2.it/MAP.
Highlights
MicroRNAs are noncoding, single-stranded small RNAs 18–24 nucleotides in length
microRNA Analysis Portal (MAP) fully respects the architecture of SMAC for generating/updating datasets underlying the database and performs five main operations (Fig. 1): (i) exploring the literature (PubMed) by listing the most relevant manuscripts according to the “microRNA” query; (ii) extracting and prioritizing biomedical terms that enrich each manuscript; (iii) generating gene networks where strength and reliability of interactions is proportional to the cocitation rate; (iv) extracting array-based expression data from Gene Expression Omnibus (GEO)[7] and converting it into a standard format; and (v) performing a range of bioinformatics analyses, selected according to the phenotype of the analyzed sample
Identification of M. oleifera microRNAs involved in immune processes
Summary
MicroRNAs (miRNAs) are noncoding, single-stranded small RNAs 18–24 nucleotides in length They regulate gene expression through complete or incomplete complementarity with the 3ʹ-untranslated region (3ʹ-UTR) of target mRNA. An enormous quantity of available published data makes the perfect selection of appropriate articles relevant to a specific study almost an art. It is often time-consuming and tiring and can lead to disinterest or eventual renunciation of the search if it was not carried out in a stepwise manner. MAP includes an updated version of MirCompare (2.0), a computational platform for selecting plant microRNAs according to their ability to regulate mammalian g enes[5]
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