DNA bound proteins such as transcription factors and modified histone proteins play an important role in gene regulation. Therefore, their genomic locations are of great interest. Usually, the location is measured using ChIP-seq and analyzed using a peak-caller. While replicated ChIP-seq experiments become more and more available, they are still mostly analyzed using methods based on peak-callers for single replicates. The only exception is PePr, which allows peak calling of several replicates. However, PePr does not provide quality measures to assess the result of the peak-calling process. Moreover, its underlying model might not be suitable for the conditions under which the experiments are performed. We propose a new peak-caller called `Sierra Platinum' that not only allows to call peaks for several replicates but also provides a variety of quality measures. Together with integrated visualizations, the quality measures support the assessment of the replicates and the resulting peaks. We show that Sierra Platinum outperforms methods based on single-replicate peak-callers as well as PePr using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project.
Over the last years, more and more biological data became available. Besides the pure amount of new data, also its dimensionality – the number of different attributes per data point – increased. Recently, especially the amount of data on chromatin and its modifications increased considerably. In the field of epigenetics, appropriate visualization tools designed for highlighting the different aspects of epigenetic data are currently not available. We present a tool called TiBi-Scatter enabling correlation analysis in 2D. This approach allows for analyzing multidimensional data while keeping the use of resources such as memory small. Thus, it is in particular applicable to large data sets.
TiBi-Scatter is a resource-friendly and easy to use tool that allows for the hypothesis-free analysis of large multidimensional biological data sets.
Published at the BioVis 2014