Abstract:
:Integrative analyses of genomic, epigenomic and transcriptomic features for human and various model organisms have revealed that many such features are nonrandomly distributed in the genome. Significant enrichment (or depletion) of genomic features is anticipated to be biologically important. Detection of genomic regions having enrichment of certain features and estimation of corresponding statistical significance rely on the expected null distribution generated by a permutation model. We discuss different genome-wide permutation approaches, present examples where the permutation strategy affects the null model and show that the confidence in estimating statistical significance of genome-wide enrichment might depend on the choice of the permutation approach. In those cases, where biologically relevant constraints are unclear, it is preferable to examine whether key conclusions are consistent, irrespective of the choice of the randomization strategy.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
De S,Pedersen BS,Kechris Kdoi
10.1093/bib/bbt053subject
Has Abstractpub_date
2014-11-01 00:00:00pages
919-28issue
6eissn
1467-5463issn
1477-4054pii
bbt053journal_volume
15pub_type
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