LncSEA 2.0:ãn updated platform for long non-coding RNA related setsãnd enrichmentãnalysis

Abstract

Long non-coding RNAs (lncRNAs) possessã wide range of biological functions,ãnd research has demonstrated their significance in regulating major biological processes suchãs de v elopment, differentiation,ãnd immune response. Theãcceleratingãccumulation of lncRNA research has greatly expanded our understanding of lncRNA functions. Here, we introduce LncSEA 2.0 ( http:// bio.liclab.net/ LncSEA/ index.php ),ãiming to provideã more comprehensive set of functional lncRNAsãnd enhanced enrichmentãnalysis capabilities. Compared with LncSEA 1.0, we have made the f ollo wing impro v ements: (i) We updated the lncRNA sets f or 11 categoriesãnd e xtremely e xpanded the lncRNA scopes f or each set. (ii) We newly introduced 15 functional lncRNA categories from multiple resources. This update not only includedã significantãmount of downstream regulatory data for lncRNAs, butãlso co v ered numerous epigenetic regulatory data sets, including lncRNA-related transcription co-factor binding, chromatin regulator binding,ãnd chromatin interaction data. (iii) We incorporated tw o ne w lncRNA set enrichmentãnalysis functions based on GSEAãnd GSVA. (iv) Weãdopted the snak emak eãnaly sis pipeline to track data processingãndãnalysis. In summary, LncSEA 2.0 offersã more comprehensive collection of lncRNA setsãndã greater variety of enrichmentãnalysis modules,ãssisting researchers inã more comprehensive study of the functional mechanisms of lncRNAs.