Data Resource And Analysis Platform Based For RNA Subcellular Localization,interaction And Function

Background and objective:Evidence accumulated over the past few decades shows that RNA has key roles in process of cells.Many RNAs perform a variety of biological functions such as modulating chromatin function,interfering with signaling pathways and regulating protein expression by interacting with RNA,protein,compound and other types of molecules.At the subcellular level,significant differences of the expression in the same RNA at different locations were found,and these differences were subsequently confirmed to has specific biological significance.Recent studies have begun to unravel how the biogenesis of RNAs that linked with their specific subcellular localizations and interactions.Many of these functions ultimately affect gene expression in diverse pathological states,such as in neuronal disorder,immune response and cancer.And it provides the evidence for clinical targeting.With the continuous increase of data,it is urgent to develop a data resource and analysis platform with subcellular localization and related interaction at the RNA level.Therefore,this study developed a comprehensive data resource and analysis platform based for RNA subcellular localization,interaction and function,which provides a reference for indepth analysis of RNA expressed at specific subcellular locations and related interactions in diseases.It also contributes to potential therapeutic applications.Materials and methods:First,data from experimentally validated,other database sources and computationally predicted RNA subcellular localization,related interaction,and associated disease were collected through text mining and batch processing.Second,normalized the names of biomolecules,subcellular locations and diseases,and integrated them under the same framework.It provides various annotations such as RNA sequence,homology,editing site,modification site and second structure.Third,the expression of RNA in subcellular localization under different conditions and the interacted RNAs in specific biological stages were analyzed based on RNA sequencing data.Fourth,the new comprehensive confidence scoring system was defined by integrating the trust of experimental evidence,trust of the scientific community and types of tissues/cells,it evaluates the reliability of each interaction.Finally,a comprehensive data resource and analysis platform for RNA subcellular localization,interaction and function was developed based on "ModelView-Controller" framework.Results and conclusions:Our study constructed a resource that named RNALocate v2.0,which includes over 210,000 experimentally validated RNA subcellular localization data,and the different expression of RNA at specific subcellular localizations under different conditions were analyzed through RNA sequencing data.Constructed a resource that named RNAInter,which contains more than 40 million RNA-associated interactions with various annotation.And is currently the largest data repository in the field of RNA interactome.At the same time,a scoring system for calculating the comprehensive confidence of each entry has been developed.Constructed a resource that named MNDR v3.0,which stores the interaction between non-coding RNAs and diseases,and embedded a variety of prediction algorithms.RNALocate v2.0,RNAInter and MNDR v3.0 can provide various functions such as data browse,query,download and prediction through the interactive operation of the website.Data among the three resources are interconnected and complemented,it constitutes a comprehensive data resource and analysis platform integrating location,interaction and function.It is helpful to explore the role of RNA in physiological and pathological conditions and to find new therapeutic targets for diseases.