Abstract
Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. Results: We present Expresso (database and webserver) as a tool for the collection and integration of available Arabidopsis ChIP-Seq peak data, which in turn can be linked to a user's gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Availability: Expresso is freely available at http://bioinformatics.cs.vt.edu/expresso/.
Highlights
Chromatin immunoprecipitation (ChIP) is a method to investigate DNA-binding sites of DNA-binding proteins, such as transcription factors (TFs) (Valouev et al, 2008)
We report on the curation of the Expresso database to collect and integrate Arabidopsis ChIP-Seq data, which in turn can be linked to a user-provided Arabidopsis gene expression data
The Expresso computational analysis pipeline comprises preprocessing of peak loci reported by at each reference dataset, finding conserved motifs using MEME-suite (Bailey et al, 2009), identifying potential target genes for each transcription factor, and storing target genes and motifs linked to TFs into the database
Summary
Chromatin immunoprecipitation (ChIP) is a method to investigate DNA-binding sites of DNA-binding proteins, such as transcription factors (TFs) (Valouev et al, 2008). Genome-wide profiling of protein binding sites is produced by either genome-tiling arrays (ChIP-ChIP) or next-generation sequencing technologies (ChIP-Seq) (Kaufmann et al, 2010; Valouev et al, 2008). ChIP-Seq has displaced ChIP-ChIP rapidly and is currently the most widely used technology for studying the action of transcription factors (Park, 2009; Valouev et al, 2008)
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