SEAweb: the Small RNA Expression Atlas Web Application

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Oct 11

PMID 31598718

Citations 9

Authors

Raza-Ur Rahman

Anna-Maria Liebhoff

Vikas Bansal

Maksims Fiosins

Ashish Rajput

Abdul Sattar

Daniel S Magruder

Sumit Madan

Ting Sun

Abhivyakti Gautam

Sven Heins

Timur Liwinski

Jorn Bethune

Claudia Trenkwalder

Juliane Fluck

Brit Mollenhauer

Stefan Bonn

Affiliations

Soon will be listed here.

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.

Citing Articles

Pathogen detection in RNA-seq data with Pathonoia.

Liebhoff A, Menden K, Laschtowitz A, Franke A, Schramm C, Bonn S BMC Bioinformatics. 2023; 24(1):53.

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isomiRdb: microRNA expression at isoform resolution.

Aparicio-Puerta E, Hirsch P, Schmartz G, Fehlmann T, Keller V, Engel A Nucleic Acids Res. 2022; 51(D1):D179-D185.

PMID: 36243964 PMC: 9825445. DOI: 10.1093/nar/gkac884.

A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids.

Alsop E, Meechoovet B, Kitchen R, Sweeney T, Beach T, Serrano G Front Cell Dev Biol. 2022; 10():804164.

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piRNAs and PIWI Proteins as Diagnostic and Prognostic Markers of Genitourinary Cancers.

Hanusek K, Poletajew S, Kryst P, Piekielko-Witkowska A, Boguslawska J Biomolecules. 2022; 12(2).

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Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions.

Rincon-Riveros A, Morales D, Rodriguez J, Villegas V, Lopez-Kleine L Int J Mol Sci. 2021; 22(21).

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