ToPASeq – an R package for topology-based pathway analysis of microarray and RNA-Seq data

Pathway analysis methods, in which differentially expressed genes are mapped to databases of reference pathways and relative enrichment is assessed, help investigators to propose biologically relevant hypotheses. The last generation of pathway analysis methods takes into account the topological structure of a pathway, which helps to increase both specificity and sensitivity of the findings. Simultaneously, the RNA-Seq technology is gaining popularity and becomes widely used for gene expression profiling. Unfortunately, majority of topological pathway analysis methods remains without implementation and if an implementation exists, it is limited in various factors.

Researchers from Masaryk University, Czech Republic developed a new R/Bioconductor package ToPASeq offering uniform interface to seven distinct topology-based pathway analysis methods, three of which they implemented de-novo and four were adjusted from existing implementations. Apart from this, ToPASeq offers a set of tailored visualization functions and functions for importing and manipulating pathways and their topologies, facilitating the application of the methods on different species. The package can be used to compare the differential expression of pathways between two conditions on both gene expression microarray and RNA-Seq data. It also provides specific tools for visualization of the results.



Visualization of the results after merging some of the gene families into one node. Some of the genes families present in the pathway were merged into single nodes. Those nodes are drawn as pie-chart, in which the number of slices equals to the number of gene merged. The colour, border and radius are preserved from the complete graph. Average log fold-change is used as representative value, when the agreement between expression and interaction type is assessed.

Availability – The package is written in R and is available from Bioconductor 3.2 using AGPL-3 license.

Ihnatova I, Budinska E. (2015) ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data. BMC Bioinformatics 16:350. [article]

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