On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Dokumenter

Hans-Ioan Ienasescu, Kang Li, Robin Andersson, Morana Vitezic, Sarah Rennie, Yun Chen, Kristoffer Vitting-Seerup, Emil Lagoni, Mette Boyd, Jette Bornholdt Lange, Michiel J. L. de Hoon, Hideya Kawaji, Timo Lassmann, FANTOM Consortium, Yoshihide Hayashizaki, Alistair R. R. Forrest, Piero Carninci, Albin Gustav Sandelin

Genomics consortia have produced large datasets profiling the expression of genes, micro-RNAs, enhancers and more across human tissues or cells. There is a need for intuitive tools to select subsets of such data that is the most relevant for specific studies. To this end, we present SlideBase, a web tool which offers a new way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders. With the help of sliders, SlideBase enables users to define custom expression thresholds for individual cell types/tissues, producing sets of genes, enhancers etc. which satisfy these constraints. Changes in slider settings result in simultaneous changes in the selected sets, updated in real time. SlideBase is linked to major databases from genomics consortia, including FANTOM, GTEx, The Human Protein Atlas and BioGPS.Database URL: http://slidebase.binf.ku.dk.

OriginalsprogEngelsk
Artikelnummerbaw144
TidsskriftDatabase
Vol/bind2016
Udgave nummer0
Antal sider10
ISSN1758-0463
DOI
StatusUdgivet - 2016

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