Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data

Methods Mol Biol. 2017:1629:271-282. doi: 10.1007/978-1-4939-7125-1_17.

Abstract

A transcription factor (TF) is a DNA binding protein that targets specific binding-sites (TFBSs) to regulate the transcript levels of its downstream genes. Thus, identifying the TF-TFBS pairs is a pivotal step in understanding the function of TFs and the regulatory network in an organism. Here, we describe two methods for predicting the TFBS of a given TF and for predicting the cognate TF of a given TFBS from a set of strongly co-expressed genes, using time-course transcriptome data of maize developing leaves.

Keywords: Cis elements; Cognate transcription factor; Gene co-expression; Gene set analysis; Transcriptome.

MeSH terms

  • Binding Sites*
  • Computational Biology / methods*
  • Conserved Sequence
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • Genes, Plant
  • Nucleotide Motifs
  • Position-Specific Scoring Matrices
  • Protein Binding
  • Software
  • Transcription Factors / metabolism*
  • Transcriptome
  • Web Browser
  • Workflow
  • Zea mays / genetics

Substances

  • Transcription Factors