TY  - JOUR
AU  - Rahman, Raza-Ur
AU  - Liebhoff, Anna-Maria
AU  - Bansal, Vikas
AU  - Fiosins, Maksims
AU  - Rajput, Ashish
AU  - Sattar, Abdul
AU  - Magruder, Daniel S
AU  - Madan, Sumit
AU  - Sun, Ting
AU  - Gautam, Abhivyakti
AU  - Heins, Sven
AU  - Liwinski, Timur
AU  - Bethune, Jörn
AU  - Trenkwalder, Claudia
AU  - Fluck, Juliane
AU  - Mollenhauer, Brit
AU  - Bonn, Stefan
TI  - SEAweb: the small RNA Expression Atlas web application.
JO  - Nucleic acids research
VL  - 48
IS  - D1
SN  - 0305-1048
CY  - London
PB  - Information Retrieval Ltd.21517
M1  - DZNE-2020-00424
SP  - D204-D219
PY  - 2020
AB  - 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.
KW  - Animals
KW  - Bacterial Infections: microbiology
KW  - Cattle
KW  - Databases, Nucleic Acid
KW  - Humans
KW  - Internet
KW  - Mice
KW  - Organ Specificity
KW  - Parkinson Disease: blood
KW  - RNA, Bacterial: metabolism
KW  - RNA, Small Untranslated: metabolism
KW  - RNA, Viral: metabolism
KW  - Rats
KW  - Virus Diseases: virology
KW  - RNA, Bacterial (NLM Chemicals)
KW  - RNA, Small Untranslated (NLM Chemicals)
KW  - RNA, Viral (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:31598718
C2  - pmc:PMC6943056
DO  - DOI:10.1093/nar/gkz869
UR  - https://pub.dzne.de/record/145065
ER  -