title: A property-based analysis of human transcription factors.
abstract: BACKGROUND
  Transcription factors are essential proteins for regulating gene expression. This regulation depends upon specific features of the transcription factors, including how they interact with DNA, how they interact with each other, and how they are post-translationally modified. Reliable information about key properties associated with transcription factors will therefore be useful for data analysis, in particular of data from high-throughput experiments.
  
  
  RESULTS
  We have used an existing list of 1978 human proteins described as transcription factors to make a well-annotated data set, which includes information on Pfam domains, DNA-binding domains, post-translational modifications and protein-protein interactions. We have then used this data set for enrichment analysis. We have investigated correlations within this set of features, and between the features and more general protein properties. We have also used the data set to analyze previously published gene lists associated with cell differentiation, cancer, and tissue distribution.
  
  
  CONCLUSIONS
  The study shows that well-annotated feature list for transcription factors is a useful resource for extensive data analysis; both of transcription factor properties in general and of properties associated with specific processes. However, the study also shows that such analyses are easily biased by incomplete coverage in experimental data, and by how gene sets are defined.
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, P.O. Box 8905, , NO-7491, Trondheim, Norway. shahram.bahrami@ntnu.no.|St. Olavs Hospital, NO-7006, Trondheim, Norway. shahram.bahrami@ntnu.no.
authors.forename: Shahram
authors.initials: S
authors.lastname: Bahrami
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, P.O. Box 8905, , NO-7491, Trondheim, Norway. rezvan.ehsani@ntnu.no.
authors.forename: Rezvan
authors.initials: R
authors.lastname: Ehsani
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, P.O. Box 8905, , NO-7491, Trondheim, Norway. finn.drablos@ntnu.no.
authors.forename: Finn
authors.initials: F
authors.lastname: Drabløs
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000378:metabolism; D006801:Humans; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA