Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. This is reflected by the many publications and database resources describing knowledge about TFs. We previously launched the TFCheckpoint database, an integrated resource focused on human, mouse and rat dbTFs, providing users access to a comprehensive overview of these proteins. Here, we describe TFCheckpoint 2.0 (https://www.tfcheckpoint.org/index.php), comprising 13 collections of dbTFs, coTFs and GTFs. TFCheckpoint 2.0 provides an easy and versatile cross-referencing system for users to view and download collections that may otherwise be cumbersome to find, compare and retrieve.
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| http://dx.doi.org/10.1093/nar/gkad1030 | DOI Listing |
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TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat.
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Department of Biology, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway.
Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. This is reflected by the many publications and database resources describing knowledge about TFs. We previously launched the TFCheckpoint database, an integrated resource focused on human, mouse and rat dbTFs, providing users access to a comprehensive overview of these proteins.
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Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
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Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge in databases is crucial for exploiting existing background knowledge, both for designing follow-up experiments and for interpreting new experimental data. Structured resources also underpin the computational integration and modeling of regulatory pathways, which further aids our understanding of regulatory dynamics.
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Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7489 Trondheim, Norway.
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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.
Summary: 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).
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