PlantPAN 3.0


The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.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. The current PlantPAN release (version 3.0) contains 17,230 TFs and 4,703 matrices of TF binding sites among 78 plant species.

For optimal use of this database, we recommend to use Google Chrome or Firefox browser and above at 1680 x 1050 resolution. Other resolution

★★★★★  PlantPAN 3.0 TF position weight matrix download is available.  ★★★★★

   

Citation:
Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chiang-Hsieh, Ping-Fu Hou, Tien-Yi Yang, and Wen-Chi Chang "PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants", Nucleic Acids Res. 2016: 44(D1):D1154-60.


Gene Search
TF/TFBS Search
Gene Group Analysis
Promoter Analysis
Cross Species
ChIP-seq Search

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.
3. Visualization of experimental regulatory factor binding sites in JBrowse.

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

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

Cross Species

  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).

ChIP-seq Search

ABOUT


Citation:

    ✎
Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chiang-Hsieh, Ping-Fu Hou, Tien-Yi Yang, and Wen-Chi Chang "PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants" Nucleic Acids Res. 2016 : 44(D1):D1154-60.

    ✎
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.





The overview of PlantPAN 3.0:



Abstract:

    The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting important regulatory elements (transcription factors binding sites (TFBSs), CpG islands, Tandem repeats, and conserved regions) and transcription factors (TFs) in a promoter or a set of promoters in plants. In this release, 17,230 TFs were collected from 78 plant species. Since ChIP-seq became a powerful technique to explore the regulatory landscape in genome, genomic locations of TFBSs were captured from 662 public ChIP-seq samples by using uniformly data processing in this study. The 1,233,999 regulatory linkages were identified among target genes and 99 regulatory factors (TFs, histones, and other DNA-binding proteins) across seven species including A. thaliana, O. sativa, Z. mays, G. max, S. lycopersicum, G. hirsutum, and A. lyrata. Additionally, this new version increased 2,449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. Besides integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events. These enhancements included: (i) 1,107 experimentally verified TF matrices from literatures, (ii) visualization of protein sequence annotations (such as functional domains, secondary structures, post-translational modification, and variants, etc.), (iii) 3D structures of TFs and TF-DNA complexes, (iv) condition-specific co-expression networks of TFs and their target genes which were extended to four species. It is not only efficient to investigate critical cis- and trans-regulatory elements in plant promoters, but also reconstruct high-confidence relationships of TF-targets under a specific condition. Confidently, the PlantPAN 3.0 will be helpful for scientists to understand complicated transcriptional regulatory networks in plants.





A comparison of PlantPAN 3.0 with previous version and the similar resources (ChIP-seq database):

Features PlantPAN 3.0 PlantPAN 2.0 PlantTFDB 4.0 ChIPBase v2.0 Expresso ReMap 2018 PCSD
No. of species in this database 78 76 165 10 1 1 3
No. of TFs 17,230 16,960 320,370 26 20 NAa 46
No. of TF matrices 4,703 1,143 674 NAa
(~6,200)b
0 0 0
No. of plant species in ChIP-seq datasets 7 0 2 1 1 0 3
No. of regulatory factors in ChIP-seq datasets 99 0 14 29
(1,414)b
20 0
(485)b
110
No. of ChIP-seq samples 662 0 NA NA NA NA NA
No. of ChIP-seq datasets 421 0 26 54
(10,216)b
20 0
(2,829)b
303
Annotation of Target genes Yes Yes No Yes Yes No Yes
Histon/Nuclesome Binding regions Yes No Yes Yes No Yes Yes
Genome Browse for binding regions Yes No Yes Yes No Yes Yes
Uniform ChIP-seq data processing Yes No Yes No No Yes Yes
Download whole genomic binding peaks (bed/bigwig files) Yes No No No No Yes Yes
Histon/Nuclesome Binding regions Yes No Yes Yes No Yes Yes
Comprehensive curation of TF information (i.e., functional domain, response conditions, target genes, activator or repressor, and sequence logos of binding motifs) Yes(increase secondary and 3D structures, PTM, and variants) Yes Yes Yes No No No
Comprehensive curation of TF information (response conditions, target genes, activator or repressor, and sequence logos of binding motifs) Yes Yes No No No Yes No
Co-expression profiles of TFs and their target genes Yes Yes No Yes Yes No No
Cis-regulatory element prediction Yes Yes Yes No No No No
a: Each TF/matrices could be accessed from the database separately. However, the total number of TFs/matrices could not be calculated via the resource.
b: The number of data for plant species is shown without brackets, whereas the total number for plant and non-plant species is indicated within brackets.





A comparison of PlantPAN 3.0 with previous version and the similar resources (Cis-regulatory elements):

Features PlantPAN 3.0 PlantPAN 2.0 PlantPAN (old) AtPAN NewPLACE AGRIS JASPAR AthaMAP
No. of plant transcription factors from different species 17230 16960 591 441 56 1770 65 NA
No. of plant species 78 76 19 1 49 1 8 1
No. of TF matrices 4,703 1143 629 NA 457 NA 65 NA
Experimentally verified TF matrices from PBM Yes Yes No No No No Yes No
Providing high-confidant TFs/TFBSs Yes Yes No Yes No No No No
Co-expression profiles of TFs and their target genes under various conditions Yes Yes No No No No No No
Protein-protein interactions between TFs and their co-factors Yes Yes No Yes No No No No
TF-target networks Yes Yes No Yes No Yes No No
The downstream promoter elements Yes 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 Yes No No No Yes
(target genes)
No No
Analysis of customized TFBS Yes Yes No No No No No No



The statistics of TFs and Matrices incorporated in nine resources and ChIP-seq dataset:

Resources Number of Regulatory factors Number of Matrices Number of Species
Uniprot 4666 44 3
CIS-BP 12802 507 44
Franco-Zorrilla et al., 2014 65 108 1
TRANSFAC (public release 7.0) 20 27 6
NewPLACE 56 457 49
JASPAR 64 64 8
Plant Cistrome Database 534 872 1
Sullivan et. al., 2015 43 46 1
UniPROBE 16 182 2
ChIP-seq dataset 99 2449 7
Total 18365 4756 122
Non-redundant in PlantPAN 3.0 17230 4703 78



Last Update: 2018/06

Contact Us


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