The Plant Promoter Analysis Navigator (PlantPAN) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands and tandem repeats) in a promoter or a set of promoters in plants. PlantPAN 4.0 provides non-redundant 3428 matrices for plant TFs in TFBS prediction and promoter sequences for 115 plant species.

NOTIFICATION
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CITATION

EXPLORE

Gene Search

  1. Identification of cis- and trans- elements of input gene.
  2. Construction of gene regulatory networks by using coexpression analysis.

TF/TFBS Search

Access TF/TFBS information by ID, matrix and keyword search (or browse by TF family and species).

Gene Group Search

  1. Determine co-occurrence TF and their binding sites within the promoters of input gene group.
  2. Regulatory network construction if co-occurrence TFs based on protein-ptotein interaction.

Promoter Analysis

TFBS scanning in the promoter sequence.

Cross Species

Identification of conserved non-coding sequences (CNSs) among homologous genes and combinational and sequences variants of TFBSs in CNSs

ChIP-seq Search

A resource that collects and utilizes plant ChIP-seq experimental data derived from GEO and SRA under various conditions to infer transcription binding sites.

GUIDE

Please click the following items to access the instructions.

Gene Search

  1. Identification of cis- and trans-elements of input gene.
  2. Construction of gene regulatory networks by using coexpression analysis.
  3. Visualization of experimental regulatory factor binding sites in JBrowse.

TF/TFBS Search

Access TF/TFBS information by ID, matrix, and keyword search (or browse by TF family and species).

Gene Group Analysis

  1. Determine co-occurrence TF and their binding sites within the promoters of input gene group.
  2. Regulatory network construction of co-occurrence TFs based on protein-protein interaction.

Promoter Analysis

TFBS scanning in the promoter sequence.

Cross Species

  1. Identification of conserved TFBSs in promoters of similar genes or user-customized promoter pairs.
  2. Construction of gene regulatory networks using homologous TFs.

ChIP-seq Search (PCBase)

  1. Access ChIP-seq data by using Gene Search, Protein Search, Genome Browser.
  2. TFBS scanning in the promoter sequence with matrices extracted from ChIP-seq peaks (Promoter Analysis).
  3. Downloading peak-calling results (BED and FASTA formats).