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Design of Knowledge Bases for Plant Gene Regulatory Networks

  • Eric Mukundi
  • Fabio Gomez-Cano
  • Wilberforce Zachary Ouma
  • Erich Grotewold
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1629)

Abstract

Developing a knowledge base that contains all the information necessary for the researcher studying gene regulation in a particular organism can be accomplished in four stages. This begins with defining the data scope. We describe here the necessary information and resources, and outline the methods for obtaining data. The second stage consists of designing the schema, which involves defining the entire arrangement of the database in a systematic plan. The third stage is the implementation, defined by actualization of the database by using software according to a predefined schema. The final stage is development, where the database is made available to users in a web-accessible system. The result is a knowledgebase that integrates all the information pertaining to gene regulation, and which is easily expandable and transferable.

Key words

Gene regulation Transcription factors Promoter Protein-DNA interaction Database design 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Eric Mukundi
    • 1
  • Fabio Gomez-Cano
    • 1
  • Wilberforce Zachary Ouma
    • 1
    • 2
  • Erich Grotewold
    • 1
    • 3
    • 4
  1. 1.Center for Applied Plant Sciences (CAPS)The Ohio State UniversityColumbusUSA
  2. 2.Molecular, Cellular and Developmental Biology Graduate ProgramThe Ohio State UniversityColumbusUSA
  3. 3.Department of Molecular Genetics and Horticulture & Crop SciencesThe Ohio State UniversityColumbusUSA
  4. 4.Department of Horticulture & Crop SciencesThe Ohio State UniversityColumbusUSA

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