title: Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control.
abstract: BACKGROUND
  Transcription factor interactions are the cornerstone of combinatorial control, which is a crucial aspect of the gene regulatory system. Understanding and predicting transcription factor interactions based on their sequence alone is difficult since they are often part of families of factors sharing high sequence identity. Given the scarcity of experimental data on interactions compared to available sequence data, however, it would be most useful to have accurate methods for the prediction of such interactions.
  
  
  RESULTS
  We present a method consisting of a Random Forest-based feature-selection procedure that selects relevant motifs out of a set found using a correlated motif search algorithm. Prediction accuracy for several transcription factor families (bZIP, MADS, homeobox and forkhead) reaches 60-90%. In addition, we identified those parts of the sequence that are important for the interaction specificity, and show that these are in agreement with available data. We also used the predictors to perform genome-wide scans for interaction partners and recovered both known and putative new interaction partners.
authors.affiliation: Applied Bioinformatics, PRI, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands.
authors.forename: A D J
authors.initials: AD
authors.lastname: van Dijk
authors.forename: C J F
authors.initials: CJ
authors.lastname: ter Braak
authors.forename: R G
authors.initials: RG
authors.lastname: Immink
authors.forename: G C
authors.initials: GC
authors.lastname: Angenent
authors.forename: R C H J
authors.initials: RC
authors.lastname: van Ham
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D020650:Combinatorial Chemistry Techniques / Q000379:methods; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D014157:Transcription Factors