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TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors

Konika Chawla, Sushil Tripathi, Liv Thommesen, Astrid Lægreid, Martin Kuiper
2013 Computer applications in the biosciences : CABIOS  
literature for references that support their function as a true sequence-specific DNA-binding RNA polymerase II TF (DbTF).  ...  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  ...  The evidence that we selected should at least support Gene Ontology term "Sequence-specific DNA-binding RNA polymerase II transcription factor activity (GO:0000981)", taking this as the minimum defining  ... 
doi:10.1093/bioinformatics/btt432 pmid:23933972 fatcat:b4ul6l6fhbdk3d7n654a6wbjea

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

Sushil Tripathi, Steven Vercruysse, Konika Chawla, Karen R. Christie, Judith A. Blake, Rachael P. Huntley, Sandra Orchard, Henning Hermjakob, Liv Thommesen, Astrid Lægreid, Martin Kuiper
2016 Database: The Journal of Biological Databases and Curation  
We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation  ...  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.  ...  DNA binding RNA polymerase II transcription factor activity (GO:0000981), or terms that are even more specific.  ... 
doi:10.1093/database/baw088 pmid:27270715 pmcid:PMC4911790 fatcat:bgvk2mjfxrcinmhz5jykd3cotq

A GO catalogue of human DNA-binding transcription factors [article]

Ruth Caroline Lovering, Pascale Gaudet, Marcio Luis Acencio, Alex Ignatchenko, Arttu Jolma, Oriol Fornes, Martin Kuiper, Ivan V Kulakovskiy, Astrid Laegreid, Maria J Martin, Colin Logie
2020 bioRxiv   pre-print
In addition, this curation effort has led to the GO annotation of almost sixty thousand DNA-binding transcription factors in over a hundred species.  ...  DNA-binding transcription factors recognise genomic addresses, specific sequence motifs in gene regulatory regions, to control gene transcription.  ...  eukaryotic protein-coding genes: 'DNA-binding transcription factor activity, RNA polymerase II-specific' (GO:0000981) (Gaudet et al., 2020a, in preparation) .  ... 
doi:10.1101/2020.10.28.359232 fatcat:j3joqptjijg5baviwglp2jqmmq