PlantPAN

PlantPAN identifies and characterizes combinatorial cis-regulatory elements, transcription factor binding sites (TFBSs), transcription factors (TFs), CpG islands, and tandem repeats in plant promoters to support reconstruction of transcriptional regulatory networks.

Key Features:

• Combinatorial cis-element identification: Identifies combinatorial cis-regulatory elements with distance constraints within co-expressed plant genes.
• TF and TFBS repository: Contains information on 16,960 TFs and 1,143 TF binding site matrices across 76 plant species, including experimentally verified TF matrices.
• Curated TF annotations: Provides curated TF information including response conditions, target genes, and sequence logos of binding motifs.
• Co-expression profiles: Supplies co-expression profiles for TFs and their target genes across various experimental conditions.
• Protein-protein interactions: Incorporates data on protein-protein interactions among TFs and their cofactors.
• TF-target networks: Constructs networks illustrating relationships between TFs and their target genes.
• Dynamic regulatory networks: Presents dynamic transcriptional regulatory networks across different conditions.
• Promoter element detection: Detects downstream promoter elements, CpG islands, and tandem repeats within plant promoters.

Scientific Applications:

• Transcriptional network reconstruction: Reconstruction of complex transcriptional regulatory networks from promoter features and TF annotations.
• TF binding characterization: Characterization of TF binding motifs and sequence logos for analysis of TF–DNA interactions.
• Condition-specific regulation analysis: Analysis of condition-dependent regulatory dynamics using co-expression profiles and dynamic networks.
• Promoter architecture analysis: Examination of promoter structural features including downstream elements, CpG islands, and tandem repeats.

Methodology:

Identification of combinatorial cis-regulatory elements with distance constraints in co-expressed genes; detection of TFBSs, CpG islands, tandem repeats, and downstream promoter elements; incorporation of curated TF annotations, experimentally verified TF binding matrices, sequence logos, co-expression profiles, protein-protein interaction data, and construction of TF-target and dynamic transcriptional regulatory networks.