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Interpreting these loci requires evaluating them with known genomic and epigenomic annotations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and\/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>GLANET can be run using its GUI or on command line. GLANET\u2019s source code is available at https:\/\/github.com\/burcakotlu\/GLANET. Tutorials are provided at https:\/\/glanet.readthedocs.org.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx326","type":"journal-article","created":{"date-parts":[[2017,5,22]],"date-time":"2017-05-22T19:19:26Z","timestamp":1495480766000},"page":"2818-2828","source":"Crossref","is-referenced-by-count":15,"title":["GLANET: genomic loci annotation and enrichment tool"],"prefix":"10.1093","volume":"33","author":[{"given":"Bur\u00e7ak","family":"Otlu","sequence":"first","affiliation":[{"name":"Department of Computer Engineering, Middle East Technical University, Ankara, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Can","family":"Firtina","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Bilkent University, Ankara, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00fcnd\u00fcz","family":"Kele\u015f","sequence":"additional","affiliation":[{"name":"Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oznur","family":"Tastan","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Bilkent University, Ankara, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,5,24]]},"reference":[{"key":"2023020206412697000_btx326-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. 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R. Stat. Soc. Ser. B (Methodological"},{"key":"2023020206412697000_btx326-B6","doi-asserted-by":"crossref","first-page":"e72.","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Benjamini","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023020206412697000_btx326-B7","doi-asserted-by":"crossref","first-page":"e13.","DOI":"10.1093\/nar\/gkp1012","article-title":"Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data","volume":"38","author":"Blahnik","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023020206412697000_btx326-B8","first-page":"3","article-title":"Teoria statistica delle classi e calcolo delle probabilit\u00e0","volume":"8","author":"Bonferroni","year":"1936","journal-title":"Pubblicazioni Del R Istituto Superiore Di Scienze Economiche e Commerciali Di Firenze"},{"key":"2023020206412697000_btx326-B9","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.1101\/gr.137323.112","article-title":"Annotation of functional variation in personal genomes using RegulomeDB","volume":"22","author":"Boyle","year":"2012","journal-title":"Genome Res"},{"key":"2023020206412697000_btx326-B10","doi-asserted-by":"crossref","first-page":"e62856.","DOI":"10.1371\/journal.pone.0062856","article-title":"Effects of GC bias in next-generation-sequencing data on de novo genome assembly","volume":"8","author":"Chen","year":"2013","journal-title":"PloS One"},{"key":"2023020206412697000_btx326-B11","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1016\/j.molcel.2014.02.032","article-title":"A Role for H3K4 monomethylation in gene repression and partitioning of chromatin readers","volume":"53","author":"Cheng","year":"2014","journal-title":"Mol. 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