Deciphering ENCODE

The ENCODE project represents a major leap from merely describing and comparing genomic sequences to surveying them for direct indicators of function. The astounding quantity of data produced by the ENCODE consortium can serve as a map to locate specific landmarks, guide hypothesis generation, and lead us to principles and mechanisms underlying genome biology. Despite its broad appeal, the size and complexity of the repository can be intimidating to prospective users. We present here some background about the ENCODE data, survey the resources available for accessing them, and describe a few simple principles to help prospective users choose the data type(s) that best suit their needs, where to get them, and how to use them to their best advantage.

TrendsHigh-throughput sequencing data have become the standard in providing evidence of function for genomic features of interest, offering a powerful way to develop hypotheses as to how they contribute to phenotypes.The ENCODE repository offers data pertinent to a broad range of genomic analyses, facilitating insights into specific phenotypes as well as genome-wide properties and principles.Despite their growing popularity, the size and complexity of the ENCODE repository can make it difficult to choose the best resources to support a given inquiry. However, considering the genomic scope and nature of an analysis can considerably simplify the choice of appropriate data.ENCODE provides a range of tools, including a web search portal, API, and integration with several popular genome browsers, to help researchers navigate the resources and retrieve the necessary data for an analysis.