Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.

ABSTRACT: Annotations of evolutionary sequence constraint based on multi-species genome alignments and genome-wide maps of epigenomic marks and transcription factor binding provide important complementary information for understanding the human genome and genetic variation. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify the evidence of each base in the genome being in an evolutionarily constrained non-exonic element from an input of over 60,000 epigenomic and transcription factor binding features. We find that the CNEP score outperforms baseline and related existing scores at predicting evolutionarily constrained non-exonic bases from such data. However, a subset of them are still not well predicted by CNEP. We developed a complementary Conservation Signature Score by CNEP

SUBMITTER: Grujic O 

PROVIDER: S-EPMC7710766 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature