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Bioinformatics. 2018 Oct 11. doi: 10.1093/bioinformatics/bty835. [Epub ahead of print]

Colocalization analyses of genomic elements: approaches, recommendations and challenges.

Kanduri C1,2, Bock C3,4,5, Gundersen S1,6, Hovig E1,6,7,8, Sandve GK1,2.

Author information

1
Department of Informatics, University of Oslo, Oslo, Norway.
2
K. G. Jebsen Coeliac Disease Research Centre, Vienna, Austria.
3
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
4
Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
5
Max Planck Institute for Informatics, Saarbr├╝cken, Germany.
6
Elixir Norway, Oslo node, University of Oslo, Oslo, Norway.
7
Department of Tumor Biology, Institute for Cancer Research, Oslo, Norway.
8
Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo, Norway.

Abstract

Motivation:

Many high-throughput methods produce sets of genomic regions as one of their main outputs. Scientists often use genomic colocalization analysis to interpret such region sets, for example to identify interesting enrichments and to understand the interplay between the underlying biological processes. Although widely used, there is little standardization in how these analyses are performed. Different practices can substantially affect the conclusions of colocalization analyses.

Results:

Here, we describe the different approaches and provide recommendations for performing genomic colocalization analysis, while also discussing common methodological challenges that may influence the conclusions. As illustrated by concrete example cases, careful attention to analysis details is needed in order to meet these challenges and to obtain a robust and biologically meaningful interpretation of genomic region set data.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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