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

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

doi:10.1093/database/baw144

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

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

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Abstract

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.

Original language	English
Article number	baw144
Journal	Database: The Journal of Biological Databases and Curation
Volume	2016
Issue number	0
Number of pages	10
ISSN	1758-0463
DOIs	https://doi.org/10.1093/database/baw144
Publication status	Published - 1 Jan 2016

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Ienasescu_2016_On-the-flyFinal published version, 1.22 MBLicence: CC BY

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Ienasescu, H.-I., Li, K., Andersson, R., Vitezic, M., Rennie, S., Chen, Y., Vitting-Seerup, K., Lagoni, E., Boyd, M., Lange, J. B., de Hoon, M. J. L., Kawaji, H., Lassmann, T., FANTOM Consortium, Hayashizaki, Y., Forrest, A. R. R., Carninci, P., & Sandelin, A. G. (2016). On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. Database: The Journal of Biological Databases and Curation, 2016(0), Article baw144. https://doi.org/10.1093/database/baw144

Ienasescu, H-I, Li, K, Andersson, R, Vitezic, M, Rennie, S, Chen, Y, Vitting-Seerup, K, Lagoni, E, Boyd, M, Lange, JB, de Hoon, MJL, Kawaji, H, Lassmann, T, FANTOM Consortium, Hayashizaki, Y, Forrest, ARR, Carninci, P & Sandelin, AG 2016, 'On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase', Database: The Journal of Biological Databases and Curation, vol. 2016, no. 0, baw144. https://doi.org/10.1093/database/baw144

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

abstract = "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.",

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

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T1 - On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

AU - Ienasescu, Hans-Ioan

AU - Li, Kang

AU - Andersson, Robin

AU - Vitezic, Morana

AU - Rennie, Sarah

AU - Chen, Yun

AU - Vitting-Seerup, Kristoffer

AU - Lagoni, Emil

AU - Boyd, Mette

AU - Lange, Jette Bornholdt

AU - de Hoon, Michiel J. L.

AU - Kawaji, Hideya

AU - Lassmann, Timo

AU - FANTOM Consortium

AU - Hayashizaki, Yoshihide

AU - Forrest, Alistair R. R.

AU - Carninci, Piero

AU - Sandelin, Albin Gustav

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N2 - 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.

AB - 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.

U2 - 10.1093/database/baw144

DO - 10.1093/database/baw144

M3 - Journal article

C2 - 28025337

SN - 1758-0463

VL - 2016

JO - Database: The Journal of Biological Databases and Curation

JF - Database: The Journal of Biological Databases and Curation

IS - 0

M1 - baw144

ER -

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

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