SKmDB: an integrated database of next generation sequencing information in skeletal muscle
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AbstractMotivation Skeletal muscles have indispensable functions and also possess prominent regenerative ability. The rapid emergence of Next Generation Sequencing (NGS) data in recent years offers us an unprecedented perspective to understand gene regulatory networks governing skeletal muscle development and regeneration. However, the data from public NGS database are often in raw data format or processed with different procedures, causing obstacles to make full use of them.Results We provide SKmDB, an integrated database of NGS information in skeletal muscle. SKmDB not only includes all NGS datasets available in the human and mouse skeletal muscle tissues and cells, but also provide preliminary data analyses including gene/isoform expression levels, gene co-expression subnetworks, as well as assembly of putative lincRNAs, typical and super enhancers and transcription factor hotspots. Users can efficiently search, browse and visualize the information with the well-designed user interface and server side. SKmDB thus will offer wet lab biologists useful information to study gene regulatory mechanisms in the field of skeletal muscle development and regeneration.
Acceptance Date23/08/2018
All Author(s) ListYuan J, Zhou JJ, Wang HT, Sun H
Journal nameBioinformatics
Year2019
Month3
Volume Number35
Issue Number5
PublisherOXFORD UNIV PRESS
Pages847 - 855
ISSN1367-4803
eISSN1460-2059
LanguagesEnglish-United Kingdom
Web of Science Subject CategoriesBiochemical Research Methods;Biotechnology & Applied Microbiology;Computer Science, Interdisciplinary Applications;Mathematical & Computational Biology;Statistics & Probability;Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology;Computer Science;Mathematical & Computational Biology;Mathematics

Last updated on 2020-03-04 at 00:50