Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data

F1000Research
Delasa AghamirzaieRuth Grene

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/.

References

May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Mar 2, 2011·BMC Genomics·Joshua W K HoPeter J Park

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Citations

Feb 20, 2019·PLoS Computational Biology·Ivar GryttenGeir K Sandve
Jan 9, 2019·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Tom MossMarianne Sabourin-Felix
Jun 1, 2018·Current Medicinal Chemistry·Tao MaLiguo Wang
Jul 28, 2020·The Plant Journal : for Cell and Molecular Biology·Dae Kwan Ko, Federica Brandizzi
Jun 18, 2020·Frontiers in Genetics·Lisa Van den BroeckRosangela Sozzani
Nov 5, 2019·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·Shubhada R Kulkarni, Klaas Vandepoele

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Methods Mentioned

BETA
immunoprecipitation
ChIP
ChIP-Seq
RNA-Seq

Software Mentioned

Expresso GitHub
MEME
suite
Expresso

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