Functional Enrichment Analysis of Regulatory Elements

Biomedicines

Pedro Carmona-Saez¹  Adrian Garcia-Moreno¹  Juan Antonio Villatoro-García¹  Alberto Ramirez-Mena¹  Raul López-Domínguez¹  Alberto Pascual-Montano²  Ernesto Aparicio-Puerta³  Michael Hackenberg³ 

[1] Bioinformatics Unit, Centre for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain;Data Science & Analytics at IDBS (Danaher Group), 68 Chertsey Road, Woking GU21 5BJ, UK;Department of Genetics, University of Granada, 18071 Granada, Spain;

关键词: gene set analysis;    regulation;    web tool;    enrichment analysis;    functional analysis;   

DOI  :  10.3390/biomedicines10030590

来源: DOAJ

【 摘 要 】

Statistical methods for enrichment analysis are important tools to extract biological information from omics experiments. Although these methods have been widely used for the analysis of gene and protein lists, the development of high-throughput technologies for regulatory elements demands dedicated statistical and bioinformatics tools. Here, we present a set of enrichment analysis methods for regulatory elements, including CpG sites, miRNAs, and transcription factors. Statistical significance is determined via a power weighting function for target genes and tested by the Wallenius noncentral hypergeometric distribution model to avoid selection bias. These new methodologies have been applied to the analysis of a set of miRNAs associated with arrhythmia, showing the potential of this tool to extract biological information from a list of regulatory elements. These new methods are available in GeneCodis 4, a web tool able to perform singular and modular enrichment analysis that allows the integration of heterogeneous information.

【 授权许可】

Unknown