PlantPAN 3.0

LINK

Download transcription factor position weight matrix

External sources

AtPAN (link: http://atpan.itps.ncku.edu.tw/)

ExPath (link: http://expath.itps.ncku.edu.tw/)

Annotation Database

TAIR (link: https://www.arabidopsis.org/index.jsp)

RAP-DB (link: http://rapdb.dna.affrc.go.jp/)

MSU Rice Genome Annotation Project (link: http://rice.plantbiology.msu.edu/)

MaizeGDB (link: http://www.maizegdb.org/)

Joint Genome Institute (Phytozome 12) (link: https://phytozome.jgi.doe.gov/pz/portal.html)

SoyBase (link: https://soybase.org/)

International Tomato Genome Sequencing Project
(link: https://solgenomics.net/organism/Solanum_lycopersicum/genome)

COTTONGEN (link: https://www.cottongen.org/)

Ensembl Plants (link: http://plants.ensembl.org/index.html)

Resources of ChIP-seq datasets

Gene Expression Omnibus (GEO) (link: https://www.ncbi.nlm.nih.gov/geo/)

Sequence Read Archive (SRA) (link: https://www.ncbi.nlm.nih.gov/sra)

Database of regulatory factors (transcription factor, histone, and other DNA-binding protein) and binding site

Transfac public (link: http://www.gene-regulation.com/pub/databases.html)

JASPAR (link: http://jaspar.genereg.net/)

CISPB (link: http://cisbp.ccbr.utoronto.ca/)

PlantTFDB (link: http://planttfdb.cbi.pku.edu.cn/)

UniProt (link: http://www.uniprot.org/)

NewPLACE (link: https://sogo.dna.affrc.go.jp/)

HistoneDB 2.0 (link: https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0)

ProtVista (link: http://ebi-uniprot.github.io/ProtVista/)

Protein Data Bank (RCSB PDB) (link: https://www.rcsb.org/)

Images for Plants

Arabidopsis lyrata (link: WIKIMEDIA COMMONS)
Author: NPS / Jacob W. Frank, Denali National Park and Preserve

Solanum lycopersicum (link: PEXELS)
Author: Krzysztof Puszczyński

Gossypium hirsutum (link: PIXABAY)
Author: Erbs55

Glycine max (link: PIXABAY)
Author: Jing

ABOUT

Citation:

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Chi-Nga Chow, Tzong-Yi Lee, Yu-Cheng Hung, Guan-Zhen Li, Kuan-Chieh Tseng, Ya-Hsin Liu, Po-Li Kuo, Han-Qin Zheng, and Wen-Chi Chang "PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants" Nucleic Acids Res. 2019.

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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.

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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	NA^a	46
No. of TF matrices	4,703	1,143	674	NA^a (~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

		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		TFBS scanning in the promoter sequence.
		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

PlantPAN 3.0

Gene Search

TF/TFBS Search

Gene Group Analysis

Promoter Analysis

Cross Species

ChIP-seq Search