title: By the company they keep: interaction networks define the binding ability of transcription factors.
abstract: Access to genome-wide data provides the opportunity to address questions concerning the ability of transcription factors (TFs) to assemble in distinct macromolecular complexes. Here, we introduce the PAnDA (Protein And DNA Associations) approach to characterize DNA associations with human TFs using expression profiles, protein-protein interactions and recognition motifs. Our method predicts TF binding events with >0.80 accuracy revealing cell-specific regulatory patterns that can be exploited for future investigations. Even when the precise DNA-binding motifs of a specific TF are not available, the information derived from protein-protein networks is sufficient to perform high-confidence predictions (area under the ROC curve of 0.89). PAnDA is freely available at http://service.tartaglialab.com/new_submission/panda.
authors.affiliation: Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Davide
authors.initials: D
authors.lastname: Cirillo
authors.affiliation: Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Teresa
authors.initials: T
authors.lastname: Botta-Orfila
authors.affiliation: Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluís Companys, 08010 Barcelona, Spain gian.tartaglia@crg.es.
authors.forename: Gian Gaetano
authors.initials: GG
authors.lastname: Tartaglia
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D001665:Binding Sites; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D020869:Gene Expression Profiling; D006801:Humans; D011485:Protein Binding; D060066:Protein Interaction Maps; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA