The DOI matches its Crossref record.
DBD––taxonomically broad transcription factor predictions: new content and functionality
Open accessAbstract
DNA-binding domain (DBD) is a database of predicted sequence-specific DNA-binding transcription factors (TFs) for all publicly available proteomes. The proteomes have increased from 150 in the initial version of DBD to over 700 in the current version. All predicted TFs must contain a significant match to a hidden Markov model representing a sequence-specific DNA-binding domain family. Access to TF predictions is provided through http://transcriptionfactor.org, where new search options are now provided such as searching by gene names in model organisms, searching for all proteins in a particular DBD family and specific organism. We illustrate the application of this type of search facility by contrasting trends of DBD family occurrence throughout the tree of life, highlighting the clear partition between eukaryotic and prokaryotic DBD expansions. The website content has been expanded to include dedicated pages for each TF containing domain assignment details, gene names, links to external databases and links to TFs with similar domain arrangements. We compare the increase in number of predicted TFs with proteome size in eukaryotes and prokaryotes. Eukaryotes follow a slower rate of increase in TFs than prokaryotes, which could be due to the presence of splice variants or an increase in combinatorial control.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
A census of human transcription factors: function, expression and evolution
Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., & Luscombe, N. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2538 · Cited by 1,573
Self-citationGenome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.
White, J. K., Gerdin, A.-K., Karp, N. A., Ryder, E., Buljan, M., Bussell, J. N., Salisbury, J., Clare, S., Ingham, N. J., Podrini, C., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.022 · Cited by 509
Genomic signatures of evolutionary transitions from solitary to group living
Kapheim, K. M., Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., et al. (2015) · Science · doi:10.1126/science.aaa4788 · Cited by 409
Robertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., et al. (2008) · Genome Research · doi:10.1101/gr.078519.108 · Cited by 182
Pluripotency and the origin of animal multicellularity
(2019) · doi:10.1038/s41586-019-1290-4 · Cited by 146
Toolbox model of evolution of prokaryotic metabolic networks and their regulation
Maslov, S., Krishna, S., Pang, T. Y., & Sneppen, K. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903206106 · Cited by 110
Lohse, M. B., Zordan, R. E., Cain, C. W., & Johnson, A. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005911107 · Cited by 67
Weng, C., Xi, J., Li, H., Cui, J., Gu, A., Lai, S., Leskov, K., Ke, L., Jin, F., & Li, Y. (2020) · Nature Metabolism · doi:10.1038/s42255-020-00314-2 · Cited by 65
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.
Leyn, S. A., Kazanov, M. D., Sernova, N. V., Ermakova, E. O., Novichkov, P. S., & Rodionov, D. A. (2013) · Journal of Bacteriology · doi:10.1128/jb.00140-13 · Cited by 58
Hutchins, A. P., Diez, D., & Miranda-Saavedra, D. (2013) · JAK-STAT · doi:10.4161/jkst.25097 · Cited by 31
Wang, Z., & Zhang, Q. (2009) · Evolutionary Bioinformatics · doi:10.4137/ebo.s2948 · Cited by 16
Johnson, Z., Anderson, D., Cheung, M. S., & Bohutskyi, P. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1569559 · Cited by 12
A Role of Bioinformatics in Agriculture
Aslam, Z., Khattak, J. Z. K., Ahmed, M., & Asif, M. (2017) · Quantification of Climate Variability, Adaptation and Mitigation for Agricultural Sustainability · doi:10.1007/978-3-319-32059-5_17 · Cited by 11
Sun, Y., Li, J., Huang, J., Li, S., Li, Y., Lu, B., & Deng, X. (2025) · eLife · doi:10.7554/elife.96172.3 · Cited by 6
Metadata
- Authors
- Wilson, D., Charoensawan, V., Kummerfeld, S. K., & Teichmann, S. A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-12-11
- Volume
- 36
- Issue
- suppl_1
- Pages
- D88-D92
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2070072684
- Cited by
- 296
- References
- 0
- FWCI
- 8.50
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
