Katarzyna Murat 1 and Krzysztof Poterlowicz
1. Faculty of Mathematics, Physics and Informatics, University of Gdansk
2. Centre for Skin Sciences, University of Bradford Abstract
Recent studies have found that distinct poor-prognosis tumours lack genetic alterations but are epigenetically heterogeneous, pointing to the important role that multi-domain epigenetic regulation in cancer progression.
Researchers studying epigenetic regulation generated a vast amount of high-throughput sequencing data for processes such as DNA methylation, histone modifications and chromatin remodelers activity and transcriptomic profiling of non-coding DNA.
Although galaxy offers range of standalone tools that allow to investigate next generation sequencing data (i.e. Bismark, MACS, SICER, edgeR ), there is a lack of multi-layers epigenetic workflows characterizing tumor progression regulation.
Here we extend use of these software to investigate epigenetic profiling of the progressive melanoma which recognized early is almost always curable. Otherwise it spreads very quickly to other parts of the body making it one of the most deadliest cancer.
By integrating DNA methylation profiles, ChIP-Seq profiles for H3K27me3, H3K4me3, MITF and BRG1 for normal melanocytes and different stages of melanoma we were able to identify novel epigenetic switches responsible for metastatic progression of this tumor.
Results and experiences using this framework demonstrate the potential for Galaxy to be a bioinformatics solution for multi-omics cancer biomarker discovery tool.