Journal Article

SeqEnrich: A tool to predict transcription factor networks from co-expressed Arabidopsis and Brassica napus gene sets

Pulgar-Vidal, Nadège C., Walker, Philip L., Belmonte, Mark F., Becker, Michael G.

2017

Overview

Transcription factors and their associated DNA binding sites are key regulatory elements of cellular differentiation, development, and environmental response. New tools that predict transcriptional regulation of biological processes are valuable to researchers studying both model and emerging-model plant systems. SeqEnrich predicts transcription factor networks from co-expressed Arabidopsis or Brassica napus gene sets. The networks produced by SeqEnrich are supported by existing literature and predicted transcription factor-DNA interactions that can be functionally validated at the laboratory bench. The program functions with gene sets of varying sizes and derived from diverse tissues and environmental treatments. SeqEnrich presents as a powerful predictive framework for the analysis of Arabidopsis and Brassica napus co-expression data, and is designed so that researchers at all levels can easily access and interpret predicted transcriptional circuits. The program outperformed its ancestral program ChipEnrich, and produced detailed transcription factor networks from Arabidopsis and Brassica napus gene expression data. The SeqEnrich program is ideal for generating new hypotheses and distilling biological information from large-scale expression data.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Arabidopsis / Arabidopsis - genetics / Arabidopsis - metabolism / Arabidopsis Proteins - genetics / Arabidopsis Proteins - metabolism / Binding sites / Bioinformatics / Biological activity / Biology and Life Sciences / Brassica / Brassica napus - genetics / Brassica napus - metabolism / Circuits / Computer and Information Sciences / Control / Datasets / Deoxyribonucleic acid / Differentiation (biology) / Distillation / Distillation equipment / DNA / DNA binding / DNA, Plant - genetics / DNA, Plant - metabolism / Gene expression / Gene Expression Regulation, Plant / Gene regulation / Genes, Plant / Genomes / Genomics / Hypotheses / Mathematical models / Networks / Plant Proteins - genetics / Plant Proteins - metabolism / Plant resistance / Protein Interaction Maps / Proteins / Rape plants / Regulatory sequences / Research and Analysis Methods / Software / Tissues / Transcription factors / Transcription Factors - genetics / Transcription Factors - metabolism / Transcriptional Activation