PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

By Jinpu Jin, Feng Tian, Dechang Yang, Yuqi Meng, Lei Kong, Jingchu Luo, Ge Gao. Nucleic Acids Res., 2016

1,945 citations recorded by the source corpus.

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.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/e1db6637c940ea034e4482d0371e603c134f88b3

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In Plant Science

1. Ge Gao
2. Mark Stitt
3. Björn Usadel
4. Anthony M. Bolger
5. Hagit Shatkay
6. Phil Hyoun Lee

Citations in the corpus

• JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles (2021, background): “thaliana (62), 21% of these TFs have a profile in the JASPAR plants CORE collection, 22% when including the Unvalidated collection.”
• PlantRegMap: charting functional regulatory maps in plants (2019, background): “With TF binding motifs throughout the genome determined by experiments in plants (7,8) and in silico-mapped in 156 plants (6), directly scanning the TF binding motifs in the promoters of putative target genes is becoming a promising option.”
• PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants (2018, background): “0 is a useful TF repository for green plants, providing various information leading to an understanding of the functions of TFs as well as genome-wide regulatory maps for 14 TFs (8).”
• AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors (2018, methodology): “There are several databases for TFs, for example, the current most comprehensive plant TFs were well-defined and established by the PlantTFDB databases (3,4).”
• Using clusterProfiler to characterize multiomics data (2024, positive): “To explore the potential gene transcriptional regulatory mechanisms of Moso bamboo (PE) under cold conditions, we downloaded a list of transcription factor families and a table of gene GO annotations for Moso bamboo from PlantTFDB 53 .”
• MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. (2019, methodology): “As an example, for the HD-ZIP family from PlantTFDB, this has been divided into HD-ZIP I / II transcription factor , HD-ZIP III transcription factor , and HD-ZIP IV transcription factor in MapMan4, following the structure from Ariel et al. (2007).”
• hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets (2019, background): “We will maintain and regularly update hTFtarget as we did for our AnimalTFDB database, which have been maintained for more than eight years.”