MORPHEUS, a Webtool for Transcription Factor Binding Analysis Using Position Weight Matrices with Dependency.
Transcriptional networks are central to any biological process and changes affecting transcription factors or their binding sites in the genome are a key factor driving evolution. As more organisms are being sequenced, tools are needed to easily predict transcription factor binding sites (TFBS) presence and affinity from mere inspection of genomic sequences. Although many TFBS discovery algorithms exist, tools for using the DNA binding models they generate are relatively scarce and their use is limited among the biologist community by the lack of flexible and user-friendly tools. We have developed a suite of web tools (called Morpheus) based on the proven Position Weight Matrices (PWM) formalism that can be used without any programing skills and incorporates some unique features such as the presence of dependencies between nucleotides positions or the possibility to compute the predicted occupancy of a large regulatory region using a biophysical model. To illustrate the possibilities and simplicity of Morpheus tools in functional and evolutionary analysis, we have analysed the regulatory link between LEAFY, a key plant transcription factor involved in flower development, and its direct target gene APETALA1 during the divergence of Brassicales clade.
Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054, Grenoble, France.
Eugenio Gómez
EG
Minguet
Laboratoire de Biologie à Grande Echelle, CEA/INSERM U1038/UJF-Grenoble 1, IRTSV, F-38054, Grenoble, Cedex 9, France.
Stéphane
S
Segard
Laboratoire de Biologie à Grande Echelle, CEA/INSERM U1038/UJF-Grenoble 1, IRTSV, F-38054, Grenoble, Cedex 9, France.
Céline
C
Charavay
Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054, Grenoble, France.
François
F
Parcy
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D023281:Genomics; D020407:Internet; D026161:MADS Domain Proteins / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices; D011401:Promoter Regions, Genetic / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism*
C091535:AP1 protein, Arabidopsis; D029681:Arabidopsis Proteins; C074747:LFY protein, Arabidopsis; D026161:MADS Domain Proteins; D014157:Transcription Factors