Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb
Fig 5
LEG predicts bona fide limb-enhancers genome-wide.
(A) Overall enrichment scores (see Methods) for the indicated functional terms based on the proximity of the newly predicted elements to the genes annotated within each category (see also S6 Fig). (B) UCSC genome browser [25] snapshots showing the landscape at two previously in vivo validated limb-enhancers that were not part of the training set but were identified in the top 10,000 predictions. The region on the left is the ZRS (ZPA Regulatory Sequence), a known regulatory element for Shh [43]; the one on the right is an intronic enhancer of Tfap2a [44]. (C) UCSC genome browser snapshot of the Hand2 gene locus. The probability of being a limb-enhancer (Ridge model) along with the top 5,000 predictions from both the Ridge Regression (RR) and the Sum Of Ranks (SOR) combined models are shown. The four elements tested for activity in the developing limbs are highlighted in boxes (green for those showing activity in the limbs at E11.5, red if negative). LacZ reporter staining (blue) indicates enhancer activities in the fore- and hindlimb mesenchyme at E11.5. One representative whole mount picture is reported for each tested element. Pictures of a representative forelimb and hindlimb are provided for the validated enhancers. Reproducibility is indicated in brackets below each whole mount picture, along with the corresponding VISTA identifier. The ranks for both combined scores (RR, SOR) are also reported. Scale bar, 100 μm.