ArticleBriefings in bioinformatics2014
The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.
Article in Briefings in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing.Bioinformatics (Oxford, England) · 2023Article
- RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity.Computational and structural biotechnology journal · 2023Article
- Genome-Wide Study of Colocalization between Genomic Stretches: A Method and Applications to the Regulation of Gene Expression.Biology · 2022Article
- Genome-wide copy number variations in a large cohort of bantu African children.BMC medical genomics · 2021Article
- Colocalization analyses of genomic elements: approaches, recommendations and challenges.Bioinformatics (Oxford, England) · 2019Article
- Detection of RNA-DNA binding sites in long noncoding RNAs.Nucleic acids research · 2019Article
- Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis.BMC bioinformatics · 2018Article
- Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.Nucleic acids research · 2018Article
- GIGGLE: a search engine for large-scale integrated genome analysis.Nature methods · 2018Article
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- Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (The Plant cell · 2017Article
- The haploinsufficient tumor suppressor, CUX1, acts as an analog transcriptional regulator that controls target genes through distal enhancers that loop to target promoters.Nucleic acids research · 2017Article
- Significance of duon mutations in cancer genomes.Scientific reports · 2016Article
- regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.Bioinformatics (Oxford, England) · 2016Article
- Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.Nucleic acids research · 2015Article
- Patterns of somatically acquired amplifications and deletions in apparently normal tissues of ovarian cancer patients.Cell reports · 2014Article
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3 authors.
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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.
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