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

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

UWA Centre for Child Health Research (affiliated with the The Kids Research Institute Australia)

Research output: Contribution to journal › Article › peer-review

18 Citations (Scopus)

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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
Pages (from-to)	1-10
Number of pages	10
Journal	Database-The Journal of Biological Databases and Curation
Volume	2016
DOIs	https://doi.org/10.1093/database/baw144 https://doi.org/10.1093/database/baw144
Publication status	Published - 1 Jan 2016

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Ienasescu et.al., 2016 On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
© The Author(s) 2016. Published by Oxford University Press in Database Journal.
Final published version, 1.13 MBLicence: CC BY

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Ienasescu, H., Li, K., Andersson, R., Vitezic, M., Rennie, S., Chen, Y., Vitting-Seerup, K., Lagoni, E., Boyd, M., Bornholdt, J., De Hoon, M. J. L., Kawaji, H., Lassmann, T., Hayashizaki, Y., Forrest, A. R. R., Carninci, P., & Sandelin, A. (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, 1-10. Article baw144. https://doi.org/10.1093/database/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 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 Jette Bornholdt and {De Hoon}, {Michiel J.L.} and Hideya Kawaji and Timo Lassmann and Yoshihide Hayashizaki and Forrest, {Alistair R.R.} and Piero Carninci and Albin Sandelin",

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year = "2016",

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doi = "10.1093/database/baw144",

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Ienasescu, H, Li, K, Andersson, R, Vitezic, M, Rennie, S, Chen, Y, Vitting-Seerup, K, Lagoni, E, Boyd, M, Bornholdt, J, De Hoon, MJL, Kawaji, H, Lassmann, T, Hayashizaki, Y, Forrest, ARR, Carninci, P & Sandelin, A 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, baw144, pp. 1-10. https://doi.org/10.1093/database/baw144, https://doi.org/10.1093/database/baw144

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AU - Ienasescu, Hans

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 - Bornholdt, Jette

AU - De Hoon, Michiel J.L.

AU - Kawaji, Hideya

AU - Lassmann, Timo

AU - Hayashizaki, Yoshihide

AU - Forrest, Alistair R.R.

AU - Carninci, Piero

AU - Sandelin, Albin

PY - 2016/1/1

Y1 - 2016/1/1

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.

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JF - Database-The Journal of Biological Databases and Curation

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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