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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...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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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 |
format | Online Article Text |
id | pubmed-5199134 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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