Reg_interactions Track Settings
 
NCBI RefSeq Functional Elements GCF_000001635.27-RS_2024_02 regulatory interactions

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Data schema/format description and download
Source data version: NCBI Mus musculus Annotation Release GCF_000001635.27-RS_2024_02 on GRCm39 assembly
Assembly: Mouse Jun. 2020 (GRCm39/mm39)
Data last updated at UCSC: 2024-02-23 15:04:35

RefSeq Functional Elements regulatory interactions

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

Methods

Interaction data was mined from internally tracked regulatory interactions in the NCBI Gene database. Pairwise interactions were determined and represented in bigInteract file format. These interactions occur between a biological region from the RefSeq Functional Elements project and an experimentally determined target gene, or between biological regions. The biological region ranges are based on parental 'biological_region' features that may include several underlying gene regulatory or other non-genic functional features, while the target gene ranges are based on NCBI 'gene' feature annotations. The ranges in this track are derived from a relevant NCBI annotation release as indicated in the 'Data version' field in the top section of this page, or in the file download path in the table schema page.

Using the track

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 RefSeq Functional Element biological regions (FE_biol_regions) track from this track hub, alongside an appropriate RefSeq gene annotation track as found elsewhere in the genome browser track options. Detailed underlying feature annotation can be viewed in the RefSeq Functional Element features (FE_features) track from this track hub.

This track is set to 'full' display mode by default. In this mode, the track can be configured to indicate interactions as curves (default), ellipses or rectangles. To view information for each regulatory interaction, hover the mouse over the small open circle in the center of each arc to display a label in the format locus1:locus2_<interaction type string>, where locus1 is the 5'-most locus symbol (with respect to the start position and plus strand of the chromosome), locus2 is the 3'-most locus symbol, and the <interaction type string> is either:

  • regulatory_element:target_gene - locus1 is a regulatory element while locus2 is a target gene
  • target_gene:regulatory_element - locus1 is a target gene while locus2 is a regulatory element
  • regulatory_element:regulatory_element - both loci are regulatory elements

Locus symbols can also be viewed by hovering the mouse over the horizontal lines from which the arcs are derived.

Alternatively, if 'pack' display mode is selected, interactions are displayed in separate rows as thick rectangles for each locus with a thin line connecting them. Locus symbols are displayed next to the thick rectangles. The interaction type label can be viewed by hovering the mouse over anywhere on the line or rectangles. This display mode may be more desirable for viewing regions with dense or complex interactions.

The following coloration is used to display regulatory interactions:

  • Blue - interactions between a regulatory element and a target gene, irrespective of which locus is the 5'-most.
  • Red - interactions between regulatory elements.

Regulatory interactions in this track are not represented quantitatively given their diverse derivations from the literature, and thus values for all scores are set to 1.

Verification

Each interaction is supported by experimental data in the literature. Supporting publications are available in the bigInteract download file as indicated in the table schema, or may be obtained by using the Table Browser or Data Integrator data explorers, or from NCBI upon request. Please visit this link for information on how to extract data from 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

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

Additional information

Further information is available on the NCBI RefSeq Functional Elements webpage.

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.