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Helicobacter pylori is a Gram-negative bacterial pathogen colonizing the human stomach. Infection with H. pylori  causes chronic inflammation of the gastric mucosa and may lead to peptic ulceration and/or gastric cancer. Using a quantitative phosphoproteomic approach several splicing factors were found to be differentially phosphorylated upon infection (Holland et al. 2011).Functional consequences of the differential phosphorylation were analyzed using RNA-seq. Analysis revealed differntially spliced genes in the infected cells. Analysis was performed using either DEXSeq or Cufflinks. Results of this tools will be compared to an in-house approach for detection of genes with significantly altered isoform expression.

Modulation of the host cell RNA splicing program by the gastric pathogen Helicobacter pylori