| Title | PlantRegMap: charting functional regulatory maps in plants |
| Authors | Tian, Feng Yang, De-Chang Meng, Yu-Qi Jin, Jinpu Gao, Ge |
| Affiliation | Peking Univ, Sch Life Sci, State Key Lab Prot & Plant Gene Res, Ctr Bioinformat, Beijing 100871, Peoples R China Peking Univ, Beijing Adv Innovat Ctr Genom ICG, Biomed Pioneering Innovat Ctr BIOPIC, Beijing 100871, Peoples R China Peking Univ, Acad Adv Interdisciplinary Studies, Peking Tsinghua Ctr Life Sci, Beijing 100871, Peoples R China |
| Keywords | CONSERVED NONCODING SEQUENCES PROVIDES INSIGHT ARABIDOPSIS NETWORKS GENE DISCOVERY INFERENCE FEATURES ELEMENTS DNA |
| Issue Date | 8-Jan-2020 |
| Publisher | NUCLEIC ACIDS RESEARCH |
| 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 .cni) 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 ciselements 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.gaolab.arg/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems. |
| URI | http://hdl.handle.net/20.500.11897/587973 |
| ISSN | 0305-1048 |
| DOI | 10.1093/nar/gkz1020 |
| Indexed | SCI(E) Scopus |
| Appears in Collections: | 生命科学学院 生物医学前沿创新中心 前沿交叉学科研究院 |
