TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors
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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). 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. Availability: The TFcheckpoint database is freely available at www.tfcheckpoint.org Contact: martin.kuiper@ntnu.no Supplementary information: Supplementary data are available at Bioinformatics online.
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The study found 78 known or putative transcription factors among the HHMC genes, which is no overrepresentation among genes with HHMCs.
“We find 78 known or putative transcription factors among the HHMC genes (Table S9) on the modern human lineage57, which is no overrepresentation among genes with HHMCs (with 49.2% of random genes sets containing fewer HHMCs).”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [57]
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- Authors
- Chawla, K., Tripathi, S., Thommesen, L., Lægreid, A., & Kuiper, M.
- Affiliations
- Norwegian University of Science and Technology (NO)
- Corresponding author
- Kuiper, Martin
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-08-09
- Volume
- 29
- Issue
- 19
- Pages
- 2519-2520
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2111756220
- Cited by
- 98
- References
- 15
- Citations by year
- 2026: 5 · 2025: 1 · 2024: 5 · 2023: 6 · 2022: 9 · 2021: 17 · 2020: 23 · 2019: 10 · 2018: 11 · 2017: 4 · 2016: 3 · 2015: 2 · 2014: 1
- FWCI
- 0.90
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Bioinformatics (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Funders
- Kreftforeningen
- Norges Teknisk-Naturvitenskapelige Universitet
- Helse Midt-Norge
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- transcription factors, DNA-binding transcription factors, RNA polymerase II, gene regulatory networks, sequence-specific DNA binding
- MeSH terms
- Animals, DNA, Humans, Protein Binding, RNA Polymerase II, Software, Transcription Factors, Internet, Databases, Genetic
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