Advance articles alert 11 July 2019

【】1.Some comments on certain statistical aspects of the study of the microbiome
José A Ferreira, Susana Fuentes
Briefings in Bioinformatics, bbz077, https://doi.org/10.1093/bib/bbz077
Published: 10 July 2019 Article history

Abstract
This note complements and clarifies part of the work of Hawinkel et al. recently published in the journal and suggests some more or less standard tools and methods for carrying out association studies of the microbiome（微生物组）.

microbiome data, association studies, nonparametric tests, p-values, false discovery rate
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2.Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods
Mitra Ebrahimpoor, Pietro Spitali, Kristina Hettne, Roula Tsonaka, Jelle Goeman
Briefings in Bioinformatics, bbz074, https://doi.org/10.1093/bib/bbz074

Abstract
Studying sets of genomic features is increasingly popular in genomics, proteomics and metabolomics since analyzing at set level not only creates a natural connection to biological knowledge but also offers more Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods
Mitra Ebrahimpoor, Pietro Spitali, Kristina Hettne, Roula Tsonaka, Jelle Goeman
Briefings in Bioinformatics, bbz074, https://doi.org/10.1093/bib/bbz074
Published: 09 July 2019 Article history
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Abstract
Studying sets of genomic features is increasingly popular in genomics, proteomics and metabolomics since analyzing at set level not only creates a natural connection to biological knowledge but also offers more statistical power. Currently, there are two gene-set testing approaches, self-contained and competitive, both of which have their advantages and disadvantages, but neither offers the final solution. We introduce simultaneous（同时的） enrichment analysis (SEA), a new approach for analysis of feature sets in genomics and other omics based on a new unified null hypothesis, which includes the self-contained and competitive null hypotheses as special cases. We employ closed testing using Simes tests to test this new hypothesis. For every feature set, the proportion of active features is estimated, and a confidence bound is provided. Also, for every unified null hypotheses, a |$P$|-value is calculated, which is adjusted for family-wise error rate. SEA does not need to assume that the features are independent. Moreover, users are allowed to choose the feature set(s) of interest after observing the data. We develop a novel pipeline and apply it on RNA-seq data of dystrophin-deficient mdx mice, showcasing the flexibility of the method. Finally, the power properties of the method are evaluated through simulation studies