Abstract

In a single experiment, chromatin immunopre-cipitation combined with high throughput sequencing (ChIP-seq) provides genome-wide infor-mation about a given covalent histone modification or transcription factor occupancy. However, time ef-ficient bioinformatics resources for extracting bio-logical meaning out of these gigabyte-scale datasets are often a limiting factor for data interpret-ation by biologists. We created an integrated portable ChIP-seq data interpretation platform called seqMINER, with optimized performances for efficient handling of multiple genome-wide datasets. seqMINER allows comparison and integration of multiple ChIP-seq datasets and extraction of quali-tative as well as quantitative information. seqMINER can handle the biological complexity of most experi-mental situations and proposes methods to the user for data classification according to the analysed features. In addition, through multiple graphical rep-resentations, seqMINER allows visualization and modelling of general as well as specific patterns in a given dataset. To demonstrate the efficiency of seqMINER, we have carried out a comprehensive analysis of genome-wide chromatin modification data in mouse embryonic stem cells to understand the global epigenetic landscape and its change through cellular differentiation.