FILER: a framework for harmonizing and querying large-scale functional genomics knowledge

PNGC is pleased to announce the release of the FILER, a functional genomics repository developed by NIAGADS, now published in NAR Genomics and Bioinformatics. Functional genomic and annotation data such as tissue-specific regulatory/enhancer elements, transcription factor binding, chromatin states, and interactions are widely used in systems biology, genetic and genomic studies, e.g., to interpret non-coding genome-wide association study signals or to characterize the experimentally identified genomic regions. We built FILER to provide scalable, unified, high-throughput, and robust access to massive, heterogeneous functional genomic (FG) data collections (> 59,000 datasets) across > 1,000 tissue/cell types curated, harmonized, and integrated from > 20 data sources including ENCODE, GTEx, FANTOM5, NIH Roadmap Epigenomics, and other large-scale projects.

All data in FILER can be queried by tissue/cell type, biological sample, assay, genomic feature type and other data attributes. Importantly, genomic queries by intervals/regions of interest are supported with high efficiency thanks to the FILER genomic indexing and search engine. In addition to uniquely providing harmonized FG and annotation data in uniform, consistent data formats, FILER provides pre-processed data per tissue/cell type, to allow users to customize which tissues/cell types to include depending on their research questions.

FILER is also available as a stand-alone version for offline, batch processing in cloud or high-performance computing (HPC) environments. For example, FILER FG and annotation data can be integrated together with the investigation/user specific experimental data and used within custom / user high-throughput genetic and genomic analysis workflows.

Example FILER interactive heatmap for accessing overlapping data/results:

Shown is an example heatmap summarizing distribution of overlaps between the FILER data and the ChIP-seq peaks input. The interactive heatmap allows users to access and download overlap results for any particular tissue category (vertical axis) and data source (horizontal axis). Preview of overlap results (pop-up panel) includes the total number of overlaps found, and the number of datasets and individual cell/tissue types overlapping with the input genomic regions in each data source/tissue category.


Kuksa PP, Leung YY, Gangadharan P, Katanic Z, Kleidermacher L, Amlie-Wolf A, Lee C-Y, Qu L, Greenfest-Allen E, Valladares O, Wang L-S (2022) FILER: a framework for harmonizing and querying large-scale functional genomics knowledge. NAR Genomics Bioinformatics.

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