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PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants.
Chow, Chi-Nga; Lee, Tzong-Yi; Hung, Yu-Cheng; Li, Guan-Zhen; Tseng, Kuan-Chieh; Liu, Ya-Hsin; Kuo, Po-Li; Zheng, Han-Qin; Chang, Wen-Chi.
Afiliación
  • Chow CN; Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan.
  • Lee TY; School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China.
  • Hung YC; Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
  • Li GZ; Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
  • Tseng KC; Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
  • Liu YH; Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
  • Kuo PL; Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
  • Zheng HQ; Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
  • Chang WC; Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan.
Nucleic Acids Res ; 47(D1): D1155-D1163, 2019 01 08.
Article en En | MEDLINE | ID: mdl-30395277
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 1 233 999 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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Plantas / Regulación de la Expresión Génica de las Plantas / Biología Computacional / Bases de Datos Genéticas / Elementos Reguladores de la Transcripción / Secuenciación de Inmunoprecipitación de Cromatina Tipo de estudio: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Año: 2019 Tipo del documento: Article País de afiliación: Taiwán Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Plantas / Regulación de la Expresión Génica de las Plantas / Biología Computacional / Bases de Datos Genéticas / Elementos Reguladores de la Transcripción / Secuenciación de Inmunoprecipitación de Cromatina Tipo de estudio: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Año: 2019 Tipo del documento: Article País de afiliación: Taiwán Pais de publicación: Reino Unido