EXPLORE


Gene Search
TF/TFBS Search
Gene Group Analysis
Promoter Analysis
Cross Species

GUIDE


Please click the following items to access the instructions.

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

Gene Search

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

TF/TFBS Search

  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.

Gene Group Analysis

  TFBS scanning in the promoter sequence.

Promoter Analysis

  Search conserved TFBSs in homologous (orthologous and paralogous) promoters or user-customized promoter pairs.

Cross Species

ABOUT


Citation:

    ▷
Chang, W.C., Lee, T.Y., Huang, H.D., Huang, H.Y. and Pan, R.L. (2008) PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC genomics, 9, 561.





Abstract:

    Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw/) 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. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between homologous gene promoters are also identified. The current PlantPAN release (version 2.0) contains 16,960 TFs and 1,143 matrices of TF binding sites among 76 plant species. Besides update of the annotation information, adding experimentally verified TF matrices, and improvements in visualization of transcriptional regulatory networks, several new features and functions were first incorporated. These features include: (i) comprehensive curation of TF information (response conditions, target genes, and sequence logos of binding motifs, etc.), (ii) co-expression profiles of TFs and their target genes under various conditions (i.e., environmental stresses, hormone treatments, and developmental stages), (iii) protein-protein interactions among TFs and their co-factors, (iv) TF-target networks, and (v) downstream promoter elements. Furthermore, a dynamic transcriptional regulatory network under various conditions is first provided in plant resources. The PlantPAN 2.0 is the most systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.





A comparison of PlantPAN 2.0 with previous version and the similar resources:

Features PlantPAN 2.0 PlantPAN (old) AtPAN NewPLACE AGRIS JASPAR AthaMAP
No. of plant transcription factors from different species 17571 591 441 56 1770 65 NA
No. of plant species 60 19 1 49 1 8 1
No. of TF matrix 1146 629 NA 457 NA 65 NA
Experimentally verified TF matrix from PBM Yes No No No No No No
Providing high-confidant TFs/TFBSs Yes No Yes No No No No
Co-expression profiles of TFs and their target genes under various conditions Yes No No No No No No
Protein-protein interactions between TFs and their co-factors Yes No Yes No No No No
TF-target networks Yes No Yes No Yes No No
The downstream promoter elements Yes No No No No No No
Comprehensive curation of TF information (response conditions, target genes, activator or repressor, and sequence logos of binding motifs) Yes No No No Yes
(target genes)
No No
Analysis of customized TFBS Yes No No No No No No



The statistics of TFs and Matrices incorporated in six resources:

Resources Number of TFs Number of Matrices Number of Species
Uniprot 4666 44 3
CIS-BP 12802 507 44
Franco-Zorrilla et al. 65 108 1
TRANSFAC (public release 7.0) 20 27 6
NewPLACE 56 457 49
JASPAR 64 64 8
Total 17673 1207 111
Non-redundant in PlantPAN 2.0 16960 1143 76



Number of TFs and matrices from top 20 species:




Last Update: 2015/07

Contact Us


Wen-Chi Chang
Website : http://wcchang.itps.ncku.edu.tw
Email : sarah321@mail.ncku.edu.tw