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Nucleic Acids Res. 2019 Oct 10. pii: gkz869. doi: 10.1093/nar/gkz869. [Epub ahead of print]

SEAweb: the small RNA Expression Atlas web application.

Author information

1
Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.
2
German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany.
3
Genevention GmbH, 37079 Göttingen, Germany.
4
Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53757 Sankt Augustin, Germany.
5
Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany.
6
Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany.
7
Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.
8
Paracelsus-Elena-Klinik, 34128 Kassel, Germany.
9
Department of Neurosurgery, University Medical Center Göttingen, 37075 Göttingen, Germany.
10
Institute of Geodesy and Geoinformation, University of Bonn, 53115 Bonn, Germany.
11
German National Library of Medicine (ZB MED) - Information Centre for Life Sciences, 53115 Bonn, Germany.
12
Institute of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany.

Abstract

We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns. We provide evidence for SEAweb's fidelity by (i) generating a set of 591 tissue specific miRNAs across 29 tissues, (ii) finding known and novel bacterial and viral infections across diseases and (iii) determining a Parkinson's disease-specific blood biomarker signature using novel data. We believe that SEAweb's 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.

PMID:
31598718
DOI:
10.1093/nar/gkz869

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