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

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...

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Autores principales: Ienasescu, Hans, Li, Kang, Andersson, Robin, Vitezic, Morana, Rennie, Sarah, Chen, Yun, Vitting-Seerup, Kristoffer, Lagoni, Emil, Boyd, Mette, Bornholdt, Jette, de Hoon, Michiel J. L., Kawaji, Hideya, Lassmann, Timo, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Carninci, Piero, Sandelin, Albin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199134/
https://www.ncbi.nlm.nih.gov/pubmed/28025337
http://dx.doi.org/10.1093/database/baw144
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author Ienasescu, Hans
Li, Kang
Andersson, Robin
Vitezic, Morana
Rennie, Sarah
Chen, Yun
Vitting-Seerup, Kristoffer
Lagoni, Emil
Boyd, Mette
Bornholdt, Jette
de Hoon, Michiel J. L.
Kawaji, Hideya
Lassmann, Timo
Hayashizaki, Yoshihide
Forrest, Alistair R. R.
Carninci, Piero
Sandelin, Albin
author_facet Ienasescu, Hans
Li, Kang
Andersson, Robin
Vitezic, Morana
Rennie, Sarah
Chen, Yun
Vitting-Seerup, Kristoffer
Lagoni, Emil
Boyd, Mette
Bornholdt, Jette
de Hoon, Michiel J. L.
Kawaji, Hideya
Lassmann, Timo
Hayashizaki, Yoshihide
Forrest, Alistair R. R.
Carninci, Piero
Sandelin, Albin
author_sort Ienasescu, Hans
collection PubMed
description 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
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spelling pubmed-51991342017-01-06 On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase Ienasescu, Hans Li, Kang Andersson, Robin Vitezic, Morana Rennie, Sarah Chen, Yun Vitting-Seerup, Kristoffer Lagoni, Emil Boyd, Mette Bornholdt, Jette de Hoon, Michiel J. L. Kawaji, Hideya Lassmann, Timo Hayashizaki, Yoshihide Forrest, Alistair R. R. Carninci, Piero Sandelin, Albin Database (Oxford) Database Tool 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 Oxford University Press 2016-12-26 /pmc/articles/PMC5199134/ /pubmed/28025337 http://dx.doi.org/10.1093/database/baw144 Text en © The Author(s) 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Tool
Ienasescu, Hans
Li, Kang
Andersson, Robin
Vitezic, Morana
Rennie, Sarah
Chen, Yun
Vitting-Seerup, Kristoffer
Lagoni, Emil
Boyd, Mette
Bornholdt, Jette
de Hoon, Michiel J. L.
Kawaji, Hideya
Lassmann, Timo
Hayashizaki, Yoshihide
Forrest, Alistair R. R.
Carninci, Piero
Sandelin, Albin
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
title On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
title_full On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
title_fullStr On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
title_full_unstemmed On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
title_short On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
title_sort on-the-fly selection of cell-specific enhancers, genes, mirnas and proteins across the human body using slidebase
topic Database Tool
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199134/
https://www.ncbi.nlm.nih.gov/pubmed/28025337
http://dx.doi.org/10.1093/database/baw144
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