The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
Open accessAbstract
With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.
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InterProScan 5: genome-scale protein function classification
Jones, P., Binns, D., Chang, H.-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., et al. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu031 · Cited by 9,301
UniProt: a hub for protein information
The UniProt Consortium (2015) · Nucleic Acids Research · doi:10.1093/nar/gku989 · Cited by 5,106
FIMO: scanning for occurrences of a given motif
Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247
Emms, D. M., & Kelly, S. (2015) · Genome Biology · doi:10.1186/s13059-015-0721-2 · Cited by 3,408
Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis Among Eukaryotes
Riechmann, J. L., Heard, J., Martin, G., Reuber, L., Jiang, C.-Z., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O. J., Samaha, R. R., et al. (2000) · Science · doi:10.1126/science.290.5499.2105 · Cited by 2,807
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D. L., Garcia-Hernandez, M., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1090 · Cited by 2,399
TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes
Matys, V. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj143 · Cited by 2,166
MEME-ChIP: motif analysis of large DNA datasets
Machanick, P., & Bailey, T. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr189 · Cited by 1,806
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
Weirauch, M. T., Yang, A., Albu, M., Cote, A. G., Montenegro-Montero, A., Drewe, P., Najafabadi, H. S., Lambert, S. A., Mann, I., Cook, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.009 · Cited by 1,785
Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C. A., Scheffler, B. E., Stelly, D. M., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3207 · Cited by 1,722
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hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets
Zhang, Q., Liu, W., Zhang, H.-M., Xie, G.-Y., Miao, Y.-R., Xia, M., & Guo, A.-Y. (2020) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2019.09.006 · Cited by 600
Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms
Wu, S., Han, B., & Jiao, Y. (2020) · Molecular Plant · doi:10.1016/j.molp.2019.10.012 · Cited by 334
Wang, R., Shu, P., Zhang, C., Zhang, J., Chen, Y., Zhang, Y., Du, K., Xie, Y., Li, M., Ma, T., et al. (2022) · New Phytologist · doi:10.1111/nph.17618 · Cited by 283
The complex geography of domestication of the African rice Oryza glaberrima
Choi, J. Y., Zaidem, M., Gutaker, R., Dorph, K., Singh, R. K., & Purugganan, M. D. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1007414 · Cited by 66
Metadata
- Authors
- Jin, J., Tian, F., Yang, D.-C., Meng, Y.-Q., Kong, L., Luo, J., & Gao, G.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-10-24
- Volume
- 45
- Issue
- D1
- Pages
- D1040-D1045
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2533355719
- Cited by
- 2,361
- References
- 35
- FWCI
- 154.27
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. https://app.cochat.ai/papers/10.1093/nar/gkw982
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- Jin, J., Tian, F., Yang, D.-C., Meng, Y.-Q., Kong, L., Luo, J., & Gao, G. (2017). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research. https://doi.org/10.1093/nar/gkw982
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