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

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/

PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants

“… c ChIPBase v2.0: http://rna.sysu.edu.cn/chipbase/ (9). d Expresso: http://bioinformatics.cs.vt.edu/expresso/ (10). e ReMap 2018: http://remap.cisreg.eu (5).…”

“…For plant species, there are several databases devoted to collecting plant ChIP-seq data and identifying their gene regulation mechanisms. For example, Expresso was created to identify the regulatory relationships among 20 A. thaliana TFs and their target genes from public ChIP-seq data (10). PlantTFDB 4.0 is a useful TF repository for green plants, providing various information leading to an understanding of the functions of TFs as well as genome-wide regulatory maps for 14 TFs (8).…”

“…Thus, there is a strong need to set up an integrative resource to interpret complicated transcriptional regulatory networks from various datasets. To date, several databases have been developed to explore the occupancy landscapes of regulatory factors, such as, Cistrome DB (4), ReMap (5), Factorbook (6), GTRD (7), PlantTFDB (8), ChIPBase (9) and Expresso (10). However, most of such resources only support mammalian and Drosophila research, and a limited number were designed for plants.…”

Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling

“…Green and red arrows represent activation and repression, respectively. access available processed ChIP-seq data in Arabidopsis (Aghamirzaie et al, 2017).…”

Manipulation of Light Signal Transduction Factors as a Means of Modifying Steroidal Glycoalkaloids Accumulation in Tomato Leaves

“…The reduced photo-inducibility of these two genes in PIF3 antisense transgenic plants confirms the view that phytochrome signals are targeted directly to the promoters of light-inducible genes through PIF3. Aghamirzaie et al ( 2017 ) reported that Acyl-CoA oxidase (At4g16760) in the upstream MVA pathway, and sterol 4-alpha-methyl-oxidase 2-1 (At1g07420) contain PIF3 binding sites in their promoters by ChIP-chip.…”