title: CressInt: a user-friendly web resource for genome-scale exploration of gene regulation inArabidopsis thaliana.
abstract: The thale cressArabidopsis thalianais a powerful model organism for studying a wide variety of biological processes. Recent advances in sequencing technology have resulted in a wealth of information describing numerous aspects ofA. thalianagenome function. However, there is a relative paucity of computational systems for efficiently and effectively using these data to create testable hypotheses. We presentCressInt, a user-friendly web resource for exploring gene regulatory mechanisms inA. thalianaon a genomic scale. TheCressIntsystem incorporates a variety of genome-wide data types relevant to gene regulation, including transcription factor (TF) binding site models, ChIP-seq, DNase-seq, eQTLs, and GWAS. We demonstrate the utility ofCressIntby showing how the system can be used to (1) Identify TFs binding to the promoter of a gene of interest; (2) identify genetic variants that are likely to impact TF binding based on a ChIP-seq dataset; and (3) identify specific TFs whose binding might be impacted by phenotype-associated variants.CressIntis freely available at http://cressint.cchmc.org.
authors: Department of Electrical Engineering and Computing Systems, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45221; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229.
authors: Xiaoting
authors: X
authors: Chen
authors: Department of Electrical Engineering and Computing Systems, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45221; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229.
authors: Kevin
authors: K
authors: Ernst
authors: Department of Electrical Engineering and Computing Systems, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45221.
authors: Frances
authors: F
authors: Soman
authors: Department of Electrical Engineering and Computing Systems, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45221; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229.
authors: Mike
authors: M
authors: Borowczak
authors: Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229; Division of Biomedical Informatics and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229.
authors: Matthew T
authors: MT
authors: Weirauch
keywords: Arabidopsis; computational tools; functional genomics; gene regulation; systems biology; transcription factors; web server