RMSS 2017

Philip Stegmaier

Integrated Analysis of Omics Data

The geneXplain platform is a multi-omics toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The system integrates an array of biological data- and knowledge bases ranging from genomic sequence data and annotation to pathway and  molecular network resources with computational methods and algorithms from different programming languages and computing environments. These can be combined into analysis workflows, multi-step procedures that provide a way to conduct analyses efficiently and reproducibly. Equipped with application programming interfaces (APIs) as well as a graphical web interface, this analysis environment can be used by programmers and  non-programmers. The platform therefore addresses important problems researchers often face, such as storage and management of data, access to existing resources and methods as well as the combination of several of those components into possibly complex analysis processes. Here we give an overview of the software and present approaches to integrate omics data focusing on gene regulation and signal transduction. Algorithms that use knowledge about molecular interactions to infer relevant signaling pathways allow us to include information gained from omics experiment, e.g. to omit interactions involving proteins that are damaged by mutation. We show results for different types of analysis methods and omics data.