Paper Info
Title
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants.
Abstract
The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional regulatory networks for plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 plant species. To explore regulatory landscapes, genomic locations of TFBSs have been captured from 662 public ChIP-seq samples using standard data processing. A total of 1 233999 regulatory linkages were identified from 99 regulatory factors (TFs, histones and other DNA-binding proteins) and their target genes across seven species. Additionally, this new version added 2449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. In addition to integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events, including (i) 1107 experimentally verified TF matrices from the literature, (ii) gene regulation network comparison between two species, (iii) 3D structures of TFs and TF-DNA complexes and (iv) condition-specific co-expression networks of TFs and their target genes extended to four species. The PlantPAN 3.0 can not only be efficiently used to investigate critical cis- and trans-regulatory elements in plant promoters, but also to reconstruct high-confidence relationships among TF-targets under specific conditions.
Year
DOI
Venue
2019
10.1093/nar/gky1081
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Genome,Histone,Biology,DNA-binding protein,DNA,Regulation of gene expression,Candidate Disease Gene,Genetics
Journal
47
Issue
ISSN
Citations 
D1
0305-1048
1
PageRank 
References 
Authors
0.37
23
9
Name
Order
Citations
PageRank
Chi-Nga Chow192.28
Tzong-Yi Lee261737.18
Yu-Cheng Hung320.74
Guan-Zhen Li420.74
Kuan-Chieh Tseng521.07
Ya-Hsin Liu6311.91
Po-Li Kuo720.74
Han-Qin Zheng861.53
Wen-Chi Chang91488.92