SEA: The Small RNA Expression Atlas

Abstract

We present the Small RNA Expression Atlas (SEA), a web application that allows for the interactive querying, visualization, and analysis of known and novel small RNAs across ten organisms. It contains sRNA and pathogen expression information for over 4,200 published samples with standardized search terms and ontologies. In addition, SEA allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAs user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns.\n\nWe provide evidence for SEAs fidelity by (i) generating a set of 591 tissue specific miRNAs across 30 tissues, (ii) finding known and novel bacterial and viral infections across diseases, and (iii) determining a Parkinsons disease-specific blood biomarker signature using novel data.\n\nWe believe that SEAs simple semantic search interface, the flexible interactive reports, and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases, and organisms.\n\nAvailability and ImplementationSEA is implemented in Java, J2EE, spring, Django, html5, css3, JavaScript, Bootstrap, Vue.js, D3, mongodb and neo4j. It is freely available at http://sea.ims.bio/.