PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
Autor: | Feng Tian, Lei Kong, De-Chang Yang, Ge Gao, Jingchu Luo, Jinpu Jin, Yu-Qi Meng |
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Rok vydání: | 2016 |
Předmět: |
0106 biological sciences
0301 basic medicine Phenylketonurias Gene regulatory network Computational biology Web Browser Biology 01 natural sciences Workflow Evolution Molecular Set (abstract data type) 03 medical and health sciences Annotation Gene Expression Regulation Plant Databases Genetic Genetics Database Issue Gene Regulatory Networks Nucleotide Motifs Transcription factor Gene Regulation of gene expression Binding Sites Computational Biology Molecular Sequence Annotation Genomics Plants 030104 developmental biology Protein Binding Transcription Factors 010606 plant biology & botany |
Zdroj: | Nucleic Acids Research |
ISSN: | 1362-4962 0305-1048 |
Popis: | 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. |
Databáze: | OpenAIRE |
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