RT Journal Article
SR Electronic
T1 SEA: The small RNA Expression Atlas
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 133199
DO 10.1101/133199
A1 Raza-Ur Rahman
A1 Abdul Sattar
A1 Maksims Fiosins
A1 Abhivyakti Gautam
A1 Daniel Sumner Magruder
A1 Jörn Bethune
A1 Sumit Madan
A1 Juliane Fluck
A1 Stefan Bonn
YR 2017
UL http://biorxiv.org/content/early/2017/08/04/133199.abstract
AB Small RNAs (sRNAs) are important biomolecules that exert vital functions in organismal health and disease, from viruses to plants, animals, and humans. Given the ever-increasing amounts of sRNA deep sequencing data in online repositories and their potential roles in disease therapy and diagnosis, it is important to enable federated sRNA expression querying across samples, organisms, tissues, cell types, and diseases. Here we present the sRNA Expression Atlas (SEA), a web application that allows for the search of known and novel small RNAs across ten organisms using standardized search terms and ontologies. SEA contains re-analyzed sRNA expression information for over 2000 published samples, including many disease datasets and over 700 novel, high-quality predicted miRNAs. We believe that SEA's simple interface and fast search in combination with its detailed interactive reports will enable researchers to better understand the potential function and diagnostic value of sRNAs across tissues, diseases, and organisms.Availability and Implementation SEA is implemented in Java, J2EE, Python, R, PHP and JavaScript. It is freely available at http://sea.dzne.de