NCBI RefSeq Functional Elements interactions and features

This track hub displays experimentally validated NCBI RefSeq Functional Element (RefSeqFE) biological regions, features, regulatory interactions between biological regions and target genes or between biological regions and each other, and recombination partner interactions between biological regions.

The following tracks are represented:

• RefSeq Functional Element biological regions (FE_biol_regions): Biological region extents where each biological region represents one or more experimentally validated non-genic functional feature(s). Each region has a record in NCBI's Gene database, and is represented by a RefSeq sequence record with an NG_ accession prefix. Detailed metadata, including nomenclature, a region summary and RefSeq accession information, can be found within this track.
  
  
• RefSeq Functional Element features (FE_features): Underlying experimentally validated functional features that are annotated on each biological region. A variety of gene regulatory, recombination type, structural type and other miscellaneous features may be found within this track, as detailed in the feature table on the RefSeq Functional Elements website. Descriptive information, functional details, experimental evidence types and publications supporting each feature can be found within this track.
  
  
• RefSeq Functional Element recombination partners (Recomb_partners): Pairwise experimentally validated recombination interactions between RefSeq Functional Element recombination features, represented in bigInteract format. Interactions in this track are at the biological region level, not per individual feature, and thus this track is best viewed in combination with the biological regions track.
  
  
• RefSeq Functional Element regulatory interactions (Reg_interactions): Pairwise experimentally validated regulatory interactions between RefSeq Functional Element gene regulatory elements and target genes, or known interactions between regulatory elements, represented in bigInteract format. Interactions in this track are at the biological region level, not per individual feature, and thus this track is best viewed in combination with the biological regions track, also alongside a RefSeq gene annotation track, as found elsewhere in the genome browser track options.

Methods

Biological regions and associated metadata were extracted from the NCBI Gene database along with annotation locations from a relevant NCBI annotation release, which is indicated in the 'Data version' field in the track details page or in the file download path. These were converted to bigBed format with field customization according to the table schema.

RefSeq Functional Element features were extracted from GFF3 files from a relevant NCBI annotation release, which is indicated in the 'Data version' field in the track details page or in the file download path. These were converted to bigBed format with field customization according to the table schema.

Interaction data was mined from internally tracked regulatory interactions and recombination partners in the NCBI Gene database. Pairwise interactions were determined and represented in bigInteract file format. These interactions can occur between a biological region and an experimentally determined target gene, or between biological regions. For all interactions, ranges are based on parental 'biological_region' features and may include several underlying gene regulatory or other non-genic functional features, while target gene ranges are based on NCBI 'gene' feature annotations. The ranges in both interaction tracks are derived from relevant NCBI annotation releases, as indicated in the 'Data version' field in the track details pages or in file download paths.

Verification

Each represented biological region, feature or interaction is supported by experimental data in the literature. Supporting publications are available in the bigBed or bigInteract download files as indicated in the table schema for each track, or may also be obtained by using the Table Browser or Data Integrator data explorers, or from NCBI upon request. Please visit this link or this link for information on how to extract data from bigBed or bigInteract files. To take maximum advantage of experimental evidence and functional data for RefSeq Functional Elements, please explore NCBI's various data access options at this link.

Credits

All data were mined and the track hub was prepared by Dr. Catherine M. Farrell, NCBI/NLM/NIH.
Email: farrelca@ncbi.nlm.nih.gov

References

Farrell CM, Goldfarb T, Rangwala SH, Astashyn A, Ermolaeva OD, Hem V, Katz KS, Kodali VK, Ludwig F, Wallin CL, Pruitt KD, Murphy TD. RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. Genome Res. 2022 Jan;32(1):175-188. doi: 10.1101/gr.275819.121. Epub 2021 Dec 7. PMID: 34876495.