title: Arabidopsis Motif Scanner.
abstract: BACKGROUND
  The major mechanism driving cellular differentiation and organism development is the regulation of gene expression. Cis-acting enhancers and silencers have key roles in controlling gene transcription. The genomic era allowed the transition from single gene analysis to the investigation of full transcriptomes. This transition increased the complexity of the analyses and the difficulty in the interpretation of the results. In this context, there is demand for new tools aimed at the creation of gene networks that can facilitate the interpretation of Next Generation Sequencing (NGS) data.
  
  
  RESULTS
  Arabidopsis Motif Scanner (AMS) is a Windows application that runs on local computers. It was developed to build gene networks by identifying the positions of cis-regulatory elements in the model plant Arabidopsis thaliana and by providing an easy interface to assess and evaluate gene relationships. Its major innovative feature is to combine the cis-regulatory element positions, NGS and DNA Chip Arrays expression data, Arabidopsis annotations and gene interactions for the identification of gene networks regulated by transcription factors. In studies focused on transcription factors function, the software uses the expression data and binding site motifs in the regulative gene regions to predict direct target genes. Additionally, AMS utilizes DNA-protein and protein-protein interaction data to facilitate the identification of the metabolic pathways regulated by the transcription factor of interest.
  
  
  CONCLUSIONS
  Arabidopsis Motif Scanner is a new tool that helps researchers to unravel gene relations and functions. In fact, it facilitates studies focused on the effects and the impact that transcription factors have on the transcriptome by correlating the position of cis-acting elements, gene expression data and interactions.
authors.affiliation: Institute of Agricultural Biology and Biotechnology (IBBA), National Council of Research (CNR), Via Salaria Km. 29.300, Monterotondo Scalo (Roma), 00015, Italy. melegio@ibba.cnr.it.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Mele
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D001665:Binding Sites; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors
references.citation: Genome Res. 2003 Sep;13(9):2030-41
references.pmid: 12952874
references.citation: Plant Cell. 2007 May;19(5):1441-57
references.pmid: 17496117
references.citation: Nat Commun. 2012;3:1281
references.pmid: 23232411
references.citation: Science. 2012 Sep 7;337(6099):1159, 1161
references.pmid: 22955811
references.citation: Nature. 2012 Sep 6;489(7414):91-100
references.pmid: 22955619
references.citation: Mol Cell. 2014 Jul 3;55(1):5-14
references.pmid: 24996062
references.citation: Nat Rev Genet. 2014 Apr;15(4):272-86
references.pmid: 24614317
references.citation: Nature. 2013 Nov 21;503(7476):414-7
references.pmid: 24067612
references.citation: BMC Plant Biol. 2007;7:55
references.pmid: 17941993
references.citation: Nat Rev Genet. 2009 Oct;10(10):669-80
references.pmid: 19736561
references.citation: Nat Rev Genet. 2010 Jan;11(1):31-46
references.pmid: 19997069
references.citation: Nat Rev Genet. 2011 Feb;12(2):87-98
references.pmid: 21191423
references.citation: Nat Rev Genet. 2010 Jul;11(7):476-86
references.pmid: 20531367
references.citation: Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12533-8
references.pmid: 21746925
references.citation: Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):445-58
references.pmid: 21957029
references.citation: Biochim Biophys Acta. 2012 May;1819(5):454-65
references.pmid: 22406342
references.citation: J Exp Bot. 2012 Jun;63(10):3887-98
references.pmid: 22442412
references.citation: Nature. 2012 Sep 6;489(7414):57-74
references.pmid: 22955616