Plantpan3.0: A new and updated resource for reconstructing transcriptional regulatory networks from chip-seq experiments in plants

Chi Nga Chow, Tzong Yi Lee, Yu Cheng Hung, Guan Zhen Li, Kuan Chieh Tseng, Ya Hsin Liu, Po Li Kuo, Han Qin Zheng, Wen Chi Chang

Research output: Contribution to journalArticlepeer-review

63 Citations (Scopus)

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 ChIPseq samples using standard data processing. A total of 1 233 999 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.

Original languageEnglish
Pages (from-to)D1155-D1163
JournalNucleic acids research
Volume47
Issue numberD1
DOIs
Publication statusPublished - 2019 Jan 8

All Science Journal Classification (ASJC) codes

  • Genetics

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