Abstract
BackgroundAssessing pathway activity levels is a plausible way to quantify metabolic differences between various conditions. This is usually inferred from microarray expression data. Wide availability of NGS technology has triggered a demand for bioinformatics tools capable of analyzing pathway activity directly from RNA-Seq data. In this paper we introduce XPathway, a set of tools that compares pathway activity analyzing mapping of contigs assembled from RNA-Seq reads to KEGG pathways. The XPathway analysis of pathway activity is based on expectation maximization and topological properties of pathway graphs.ResultsXPathway tools have been applied to RNA-Seq data from the marine bryozoan Bugula neritina with and without its symbiotic bacterium “Candidatus Endobugula sertula”. We successfully identified several metabolic pathways with differential activity levels. The expression of enzymes from the identified pathways has been further validated through quantitative PCR (qPCR).ConclusionsOur results show that XPathway is able to detect and quantify the metabolic difference in two samples. The software is implemented in C, Python and shell scripting and is capable of running on Linux/Unix platforms. The source code and installation instructions are available at http://alan.cs.gsu.edu/NGS/?q=content/xpathway.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2823-y) contains supplementary material, which is available to authorized users.
Highlights
Assessing pathway activity levels is a plausible way to quantify metabolic differences between various conditions
B. neritina associates with an uncultured microbial symbiont, “Candidatus Endobugula sertula” [12] that has been shown to produce bryostatins, bioactive compounds that protect the host larvae from predation [13, 14]
Because of the pharmaceutical potential of the bryostatins, and the inablilty to grow the symbiont in the laboratory, we chose to examine host gene expression in the presence and absence of the symbiont to understand more about the molecular underpinnings of this relationship
Summary
Assessing pathway activity levels is a plausible way to quantify metabolic differences between various conditions. This is usually inferred from microarray expression data. Wide availability of NGS technology has triggered a demand for bioinformatics tools capable of analyzing pathway activity directly from RNA-Seq data. In this paper we introduce XPathway, a set of tools that compares pathway activity analyzing mapping of contigs assembled from RNA-Seq reads to KEGG pathways. Because of RNA-Seq, it is easier to characterize transcripts and their isoforms, to detect genes without need of prior information in the form of probes or primers, and estimate expression levels of transcripts with good precision. In contrast to microarray data, RNA-Seq data allows frequency of expression of all transcripts without a priori knowledge of the gene sequence. The Author(s) BMC Genomics 2016, 17(Suppl 5):542 existing tools incorporate this step, which is the major focus of this paper
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