PlantRegMap: charting functional regulatory maps in plants

By Feng Tian, Dechang Yang, Yuqi Meng, Jinpu Jin, Ge Gao. Nucleic Acids Res., 2019

942 citations recorded by the source corpus.

Abstract With the goal of charting plant transcriptional regulatory maps (i.e. transcription factors (TFs), cis-elements and interactions between them), we have upgraded the TF-centred database PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) to a plant regulatory data and analysis platform PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) over the past three years. In this version, we updated the annotations for the previously collected TFs and set up a new section, ‘extended TF repertoires’ (TFext), to allow users prompt access to the TF repertoires of newly sequenced species. In addition to our regular TF updates, we are dedicated to updating the data on cis-elements and functional interactions between TFs and cis-elements. We established genome-wide conservation landscapes for 63 representative plants and then developed an algorithm, FunTFBS, to screen for functional regulatory elements and interactions by coupling the base-varied binding affinities of TFs with the evolutionary footprints on their binding sites. Using the FunTFBS algorithm and the conservation landscapes, we further identified over 20 million functional TF binding sites (TFBSs) and two million functional interactions for 21 346 TFs, charting the functional regulatory maps of these 63 plants. These resources are publicly available at PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) and a cloud-based mirror (http://plantregmap.gao-lab.org/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/87d0c462620f9f70ef20960090bb2cabbf587ad7

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In Molecular Biology

1. Li Zhan
2. Tianzhi Wu
3. Wenli Tang
4. Zijing Xie
5. Shuangbin Xu
6. Xiao Luo
7. Qianwen Wang
8. Erqiang Hu

Citations in the corpus

• Using clusterProfiler to characterize multiomics data (2024, positive): “Furthermore, for intricate annotations associated with the regulatory dynamics of plant transcription factors, our reference point was the esteemed plantRegMap database 63 .”