2012
DOI: 10.1089/cmb.2011.0249
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Fast, Sensitive Discovery of Conserved Genome-Wide Motifs

Abstract: Regulatory sites that control gene expression are essential to the proper functioning of cells, and identifying them is critical for modeling regulatory networks. We have developed Magma (Multiple Aligner of Genomic Multiple Alignments), a software tool for multiple species, multiple gene motif discovery. Magma identifies putative regulatory sites that are conserved across multiple species and occur near multiple genes throughout a reference genome. Magma takes as input multiple alignments that can include gap… Show more

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Cited by 7 publications
(7 citation statements)
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“…To identify such factor(s), we examined which transcription factor binding sites were over-represented in the promoters of S. aureus- induced C. elegans genes. Using the software MAGMA (Ihuegbu et al, 2012), we analyzed the transcription start site (TSS)-proximal upstream 2 kb, and detected over-representation of the E-box DNA motif (CACGTG, P<0.001) (Fig. 1A).…”
Section: Resultsmentioning
confidence: 99%
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“…To identify such factor(s), we examined which transcription factor binding sites were over-represented in the promoters of S. aureus- induced C. elegans genes. Using the software MAGMA (Ihuegbu et al, 2012), we analyzed the transcription start site (TSS)-proximal upstream 2 kb, and detected over-representation of the E-box DNA motif (CACGTG, P<0.001) (Fig. 1A).…”
Section: Resultsmentioning
confidence: 99%
“…249 genes were identified whose probe intensity were higher than expected by chance ( 15, p < 0.01). In parallel, we discovered a catalog of 2,309 potentially functional DNA motifs with MAGMA using its default parameters (Ihuegbu et al, 2012). MAGMA uses C. elegans as the reference genome and compares segments of the genome that are conserved across five other nematode species, to identify motifs within the reference genome that occur in intergenic, intronic, and 5′ and 3′ untranslated regions of annotated genes (Ihuegbu et al, 2012).…”
Section: Methodsmentioning
confidence: 99%
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“…We also identified novel motifs in noncoding DHSs for which there were no known functions. Some of these matched conserved DNA motifs found by two prior studies (Elemento and Tavazoie 2005;Ihuegbu et al 2012). We performed Gene Ontology (GO) and anatomy enrichment analysis on genes associated with these motifs to predict potential function ( Supplemental Tables S4, S5).…”
Section: Discriminative Motif Discovery Within Noncoding Dhs Peaks Idmentioning
confidence: 72%
“…Because the genome is relatively compact, regulatory sequences are often contained within relatively short non-coding promoter regions, which are often close to the regulated gene (The C. elegans Sequencing Consortium, 1998). A number of groups have used both computational and biological techniques to elicit TFBSs and regulatory networks (Arda and Walhout, 2010); (Bigelow et al, 2004); (Hobert et al, 2010); (Ihuegbu et al, 2012); (Newburger and Bulyk, 2009); (Reece-Hoyes et al, 2005). Much information related to cell type specific gene expression has been elucidated (Bamps and Hope, 2008); (Hunt-Newbury et al, 2007), and collected in curated databases (Hope Laboratory Expression Pattern Database); (WormBase).…”
Section: Introductionmentioning
confidence: 99%