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; FANTOM Consortium; 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

Database (Oxford). 2016 Dec 26:2016:baw144. doi: 10.1093/database/baw144. Print 2016.

Authors

Hans Ienasescu^{1

2}, Kang Li^{1

2

3}, Robin Andersson¹, Morana Vitezic^{1

2}, Sarah Rennie¹, Yun Chen^{1

2}, Kristoffer Vitting-Seerup^{1

2}, Emil Lagoni^{1

2}, Mette Boyd^{1

2}, Jette Bornholdt^{1

2}, Michiel J L de Hoon⁴, Hideya Kawaji^{4

5}, Timo Lassmann^{4

6}; FANTOM Consortium; Yoshihide Hayashizaki^{4

5}, Alistair R R Forrest^{4

7}, Piero Carninci⁴, Albin Sandelin^{8

2}

Affiliations

¹ Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen N, DK2200, Denmark.
² Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen N, DK2200, Denmark.
³ Department of Mathematical Sciences, University of Copenhagen, Universitetsparken 5, Copenhagen Ø, DK2100, Denmark.
⁴ RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
⁵ RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
⁶ Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, 6008, Australia Western Australia.
⁷ Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia.
⁸ Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen N, DK2200, Denmark albin@binf.ku.dk.

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.Database URL: http://slidebase.binf.ku.dk.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Genetic*
Enhancer Elements, Genetic*
Genome, Human*
Human Genome Project
Humans
MicroRNAs / genetics*
Proteins / genetics*
Sequence Analysis, DNA / methods*

Substances

MicroRNAs
Proteins