TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors.
CONCLUSIONS
Gene regulatory network assembly and analysis requires high-quality knowledge sources that cover functional aspects of the various components of the gene regulatory machinery. A multiplicity of resources exists with information about mammalian transcription factors (TFs); yet, only few of these provide sufficiently accurate classifications of the functional roles of individual TFs, or standardized evidence that would justify the information on which these functional classifications are based. We compiled the list of all putative TFs from nine different resources, ignored factors such as general TFs, mediator complexes and chromatin modifiers, and for the remaining factors checked the available literature for references that support their function as a true sequence-specific DNA-binding RNA polymerase II TF (DbTF). The results are available in the TFcheckpoint database, an exhaustive collection of TFs annotated according to experimental and other evidence on their function as true DbTFs. TFcheckpoint.org provides a high-quality and comprehensive knowledge source for genome-scale regulatory network studies.


BACKGROUND
The TFcheckpoint database is freely available at www.tfcheckpoint.org
Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7489 Trondheim, Norway and Department of Technology, Sør-Trøndelag, University College, N-7004 Trondheim, Norway.
Konika
K
Chawla
Sushil
S
Tripathi
Liv
L
Thommesen
Astrid
A
Lægreid
Martin
M
Kuiper
D000818:Animals; D004247:DNA / Q000378:metabolism; D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D011485:Protein Binding; D012319:RNA Polymerase II / Q000032:analysis* / Q000737:chemistry; D012984:Software; D014157:Transcription Factors / Q000032:analysis* / Q000737:chemistry
D014157:Transcription Factors; D004247:DNA; D012319:RNA Polymerase II