Journal: Genome Research

Article Title: RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse

doi: 10.1101/gr.275819.121

Figure Lengend Snippet: Example of a biological region RefSeqFE flat file. Segments of RefSeq accession NG_052895.1 representing the hemoglobin subunit beta locus control region ( HBB-LCR ) are shown. ( A ) Top section of the flat file with a link to BioProject accession PRJNA343958 and the “RefSeqFE” keyword outlined in red. ( B ) Segment of the feature annotation section. Features are displayed for the 5′HS5 DNase I hypersensitive site ( Tuan et al. 1985 ; Dhar et al. 1990 ; Wai et al. 2003 ), a transcriptional cis -regulatory region ( Long et al. 1998 ), a CTCF binding site ( Farrell et al. 2002 ; Bulger et al. 2003 ; Chan et al. 2008 ), and an enhancer-blocking element ( Farrell et al. 2002 ). Features include “/experiment” qualifiers with experimental evidence from the literature as indicated by ECO strings and IDs and links to publications (blue tabs), “/note” qualifiers with descriptive information (gray tabs), “/function” qualifiers describing the function of each feature where applicable (green tabs), and a “/bound_moiety” qualifier for the protein-binding site (red tab). All features include a “/db_xref” qualifier (black tabs) linking to the biological region record in the Gene database (GeneID:109580095), and an INSDC class qualifier when relevant (orange tabs).

Article Snippet: The National Center for Biotechnology Information (NCBI) therefore provides RefSeq Functional Elements (RefSeqFEs), which represent experimentally validated human and mouse nongenic elements derived from the literature.

Techniques: Control, Binding Assay, Blocking Assay, Protein Binding

Journal: Genome Research

Article Title: RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse

doi: 10.1101/gr.275819.121

Figure Lengend Snippet: Comparison of RefSeqFEs to other gene regulatory data sets. ( A ) Overview showing data derivation, feature type representation, and current sizes of each data set on the human GRCh38.p13 and mouse GRCm39 reference assemblies. Additional information for each data set is provided in Supplemental Table S5A . ( B ) Bar graph showing human AR 109.20201120 RefSeqFE feature intersections with the indicated data sets, for which the y -axis represents the percent of input RefSeqFE features showing overlap. All features in comparative data sets were intersected with either all RefSeqFE features (medium blue bars), RefSeqFE regulatory features (gray bars), or RefSeqFE enhancer features (light blue bars). Enhancer features from each data set were additionally intersected with RefSeqFE enhancer features (dark blue bars). Full statistics including input and overlapping feature counts, overlap percentages with respect to each data set, Fisher P -values, and Jaccard statistics are provided in Supplemental Table S5B , with raw intersection output, feature lengths, and degrees of overlap with respect to each data set in Supplemental Table S5D . Data sets showing overlap with each RefSeqFE feature are also indicated in Supplemental Table S3B , column G. ( C ) Box plot showing feature length distributions for the indicated human data sets. Some outliers and dbSUPER feature lengths (maximum 498572) are not displayed because the y -axis was scaled to better visualize shorter feature distributions; see Supplemental Figure S6A for a 50-kb y -axis scale with dbSUPER data included: n = 9862, 926,535, 622,457, 63,285, and 1989 sample points. Additional statistics including minimums, maximums, averages, and standard deviations from the mean are provided in Supplemental Table S5A . ( D ) Bar graph showing mouse AR 109 RefSeqFE feature intersections with the indicated data sets, as described for human in B . Supporting details are provided in Supplemental Tables S3C and S5C,E . ( E ) Box plot showing feature length distributions for the indicated mouse data sets, as described for human in C : n = 2271, 343,747, 364,670, 49,802, and 1291 sample points. Supporting details are provided in Supplemental Table S5A and Supplemental Figure S6 .

Article Snippet: The National Center for Biotechnology Information (NCBI) therefore provides RefSeq Functional Elements (RefSeqFEs), which represent experimentally validated human and mouse nongenic elements derived from the literature.

Techniques: Comparison