Decoding the non-coding genome: Opportunities and challenges of genomic and epigenomic consortium data

Publicly-available next-generation sequencing data has greatly expanded in the past decade, particularly through the work of several international consortia. These collaborative efforts have applied numerous assays profiling diverse features of gene regulation, such as genome-wide chromatin structure, transcriptional activity, and transcription factor binding, to thousands of biosamples from several organisms. Newly-developed computational analyses and statistical methods link findings to gene expression changes and phenotypic changes. Integrative analysis of these datasets holds the potential to revolutionize our understanding of organismal development, cell type differentiation, cellular response to stimuli, and disease mechanisms. However, standardized methods for data access, uniform data processing, and integrative analysis largely do not exist, hindering the impacts of these efforts. Here we review advancements made by consortia and directions of ongoing efforts, as well as challenges in accessing and analyzing publicly-available consortium data and emerging tools for addressing these challenges.