Journal Article
. 2011 Dec; 28(3):419-20.
doi: 10.1093/bioinformatics/btr666.

GenomeRunner: automating genome exploration

Mikhail G Dozmorov 1 Lukas R Cara  Cory B Giles  Jonathan D Wren  
Affiliations
  • PMID: 22155868
  •     14 References
  •     21 citations

Abstract

Motivation: One of the challenges in interpreting high-throughput genomic studies such as a genome-wide associations, microarray or ChIP-seq is their open-ended nature-once a set of experimentally identified regions is identified as statistically significant, at least two questions arise: (i) besides P-value, do any of these significant regions stand out in terms of biological implications? (ii) Does the set of significant regions, as a whole, have anything in common genome wide? These issues are difficult to address because of the growing number of annotated genomic features (e.g. single nucleotide polymorphisms, transcription factor binding sites, methylation peaks, etc.), and it is difficult to know a priori which features would be most fruitful to analyze. Our goal is to provide partial automation of this process to begin examining associations between experimental features and annotated genomic regions in a hypothesis-free, data-driven manner.

Results: We created GenomeRunner-a tool for automating annotation and enrichment of genomic features of interest (FOI) with annotated genomic features (GFs), in different organisms. Besides simple association of FOIs with known GFs GenomeRunner tests whether the enriched FOIs, as a group, are statistically associated with a large and growing set of genomic features.

Availability: GenomeRunner setup files and source code are freely available at http://sourceforge.net/projects/genomerunner.

Contact: mikhail-dozmorov@omrf.org; Jonathan-Wren@omrf.org; jdwren@gmail.com

Supplementary Information: Supplementary data are available at Bioinformatics online.

Automating genomic data mining via a sequence-based matrix format and associative rule set.
Jonathan D Wren, David Johnson, Le Gruenwald.
BMC Bioinformatics, 2005 Jul 20; 6 Suppl 2. PMID: 16026599    Free PMC article.
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, +8 authors, Jill P Mesirov.
Proc Natl Acad Sci U S A, 2005 Oct 04; 102(43). PMID: 16199517    Free PMC article.
Highly Cited.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium, Ewan Birney, +316 authors, Pieter J de Jong.
Nature, 2007 Jun 16; 447(7146). PMID: 17571346    Free PMC article.
Highly Cited.
Testing association between disease and multiple SNPs in a candidate gene.
W James Gauderman, Cassandra Murcray, Frank Gilliland, David V Conti.
Genet Epidemiol, 2007 Apr 06; 31(5). PMID: 17410554
Highly Cited.
An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Hongkai Ji, Hui Jiang, +3 authors, Wing H Wong.
Nat Biotechnol, 2008 Nov 04; 26(11). PMID: 18978777    Free PMC article.
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A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide.
Jonathan D Wren.
Bioinformatics, 2009 May 19; 25(13). PMID: 19447786    Free PMC article.
The UCSC Table Browser data retrieval tool.
Donna Karolchik, Angela S Hinrichs, +4 authors, W James Kent.
Nucleic Acids Res, 2003 Dec 19; 32(Database issue). PMID: 14681465    Free PMC article.
Highly Cited.
Insights into colon cancer etiology via a regularized approach to gene set analysis of GWAS data.
Lin S Chen, Carolyn M Hutter, +4 authors, Li Hsu.
Am J Hum Genet, 2010 Jun 22; 86(6). PMID: 20560206    Free PMC article.
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.
Jeremy Goecks, Anton Nekrutenko, James Taylor, Galaxy Team.
Genome Biol, 2010 Aug 27; 11(8). PMID: 20738864    Free PMC article.
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Melissa S Cline, Rachel Karchin.
Bioinformatics, 2010 Dec 17; 27(4). PMID: 21159622    Free PMC article.
Review.
Critical association of ncRNA with introns.
David Rearick, Ashwin Prakash, +3 authors, Alexei Fedorov.
Nucleic Acids Res, 2010 Nov 13; 39(6). PMID: 21071396    Free PMC article.
Pathway-based approaches for analysis of genomewide association studies.
Kai Wang, Mingyao Li, Maja Bucan.
Am J Hum Genet, 2007 Oct 30; 81(6). PMID: 17966091    Free PMC article.
Highly Cited.
DAVID: Database for Annotation, Visualization, and Integrated Discovery.
Glynn Dennis, Brad T Sherman, +4 authors, Richard A Lempicki.
Genome Biol, 2003 May 08; 4(5). PMID: 12734009
Highly Cited.
GREAT improves functional interpretation of cis-regulatory regions.
Cory Y McLean, Dave Bristor, +5 authors, Gill Bejerano.
Nat Biotechnol, 2010 May 04; 28(5). PMID: 20436461    Free PMC article.
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Angélica M Delgado-Vega, Mikhail G Dozmorov, +21 authors, Marta E Alarcón-Riquelme.
Ann Rheum Dis, 2012 Jun 15; 71(7). PMID: 22696686    Free PMC article.
Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome.
Christopher J Lessard, He Li, +58 authors, Kathy L Sivils.
Nat Genet, 2013 Oct 08; 45(11). PMID: 24097067    Free PMC article.
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Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes.
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Epigenetics, 2013 Nov 12; 9(2). PMID: 24213554    Free PMC article.
Systematic classification of non-coding RNAs by epigenomic similarity.
Mikhail G Dozmorov, Cory B Giles, Kristi A Koelsch, Jonathan D Wren.
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Kunlin Zhang, Suhua Chang, Liyuan Guo, Jing Wang.
Protein Cell, 2014 Nov 20; 6(3). PMID: 25407412    Free PMC article.
Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes.
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Edwin J C G van den Oord, Shaunna L Clark, +7 authors, Karolina A Aberg.
Schizophr Bull, 2015 Dec 15; 42(4). PMID: 26656881    Free PMC article.
High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction.
Joseph L McClay, Andrey A Shabalin, +11 authors, Edwin J C G van den Oord.
Genome Biol, 2015 Dec 25; 16. PMID: 26699738    Free PMC article.
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Review.
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Sexually divergent DNA methylation patterns with hippocampal aging.
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