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[Preprint]. 2023 Dec 27:2023.12.22.23300468. [Version 1] doi: 10.1101/2023.12.22.23300468

Extended Data Figure 6. Toggling input data for Activity-by-Contact enhancer prediction.

Extended Data Figure 6.

a. Whole mount in vivo enhancer reporter expression for the seven VISTA Enhancers that are annotated for cranial nerve (CN) expression, inspected for and have CN7 expression, and have positive Activity-by-Contact (ABC) enhancer predictions for CN7 at e11.5. Peak-to-gene predictions match ABC predictions in all cases (7/7). Replacing CN7 e11.5 H3K27Ac or ATAC data with these data from a distantly related cell type (mouse embryonic limb e11.5) results in either a matching or a non-matching cognate gene prediction. Substituting cMN7 e11.5 histone modification data with “Limb H3K27Ac” histone modification data alters predictions for 3 out of 7 enhancers. Substituting cMN7 scATAC data with “Limb ATAC” data alters predictions for 6 out of 7 enhancers. Neither substituted input correctly identifies the CREST1 enhancer (VISTA enhancer hs1419). Positive evidence of CN7 enhancement is depicted by arrows.

b. Stacked barplot summarizing consequences of toggled input data.