PlantRegMap: Plant Regulation Data and Analysis Platform @ CBI, PKU

PlantTFDB

Plant Transcriptional Regulatory Map

Our mission is to provide a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them, advancing the understanding of plant transcriptional regulatory system.

Transcription Factors

Comprehensive family assignment rules for plant TFs.

A TF knowledge base covering main lineages of green plants.

TFext - Extended TF repertoires for newly sequenced species.

A set of manually curated, non-redundant, high-quality TF binding motifs derived from experiments.

Regulatory Landscape

Multiple types of regulatory elements derived from high-throughput assays and genome comparison.

Genome-wide regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements.

ATRM - Architectures and evolutionary features of plant transcription regulatory systems.

Prediction and Analysis Tools

BLAST - Aligning protein or nucleic acids sequences to plant TFs.

TF prediction - Identifying TFs from protein or nucleic acids sequences.

ID mapping - Mapping input IDs to PlantRegMap IDs through BLAST.

Binding site prediction - Scanning TF binding sites from input sequences.

FunTFBS - An algorithm to screen for functional TF binding sites.

Regulation prediction - Inferring interactions and finding the enriched upstream regulators.

GO enrichment - Finding over-represented GO terms based on systemic GO annotation of genes.

TF enrichment - Finding TFs whose targets are over-represented in your gene set.

Evolution and Conservation

Orthologous groups and RBHs for all genes of 156 plant species.

A set of pairwise and multiple genome alignments for 63 plants in 7 lineages.

Genome-wide conserved elements and conservation scores (PhastCons and PhyloP) for 63 plants.

[中文版本]

How to Cite:

Tian, F., Yang, D.C., Meng, Y.Q., Jin, J. and Gao, G. (2020) PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res 48, D1104-D1113.
Jin, J., Tian, F., Yang, D.C., Meng, Y.Q., Kong, L., Luo, J. and Gao, G. (2017) PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res, 45, D1040-D1045.
Jin, J., He, K., Tang, X., Li, Z., Lv, L., Zhao, Y., Luo, J. and Gao, G. (2015) An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Mol Biol Evol, 32, 1767-1773.