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Nucleic Acids Res. 2017 Jul 3;45(W1):W109-W115. doi: 10.1093/nar/gkx329.

WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes.

Author information

1
Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy.
2
Institute of Biomedical Technologies, National Research Council, 70126, Bari, Italy.
3
Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, 41125, Modena, Italy.
4
IFOM, the FIRC Institute of Molecular Oncology, 20139, Milan, Italy.
5
Institute of Molecular Genetics, National Research Council, 27100, Pavia, Italy.

Abstract

The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria. RNA-sequencing or microarray-based gene expression data are provided as input, along with gene annotations. The user can select genomic annotations from an internal database including 2780 bacterial strains, or provide custom genomic annotations. The analysis produces as output the lists of positionally related genes showing a coordinated trend of differential expression. Graphical representations, including a circular plot of the analyzed chromosome, allow intuitive browsing of the results. The analysis procedure is based on our previously published R-package PREDA. The release of this tool is timely and relevant for the scientific community, as WoPPER will fill an existing gap in prokaryotic gene expression data analysis and visualization tools. WoPPER is open to all users and can be reached at the following URL: https://WoPPER.ba.itb.cnr.it.

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