2020
DOI: 10.1101/2020.10.22.351049
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Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

Abstract: Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cell types, while the accuracy of genome-wide approaches remains elusive due to the lack of a systematic evaluation. We combined multiple spatial and in silico approaches for defining enhancer locations and linking them to their target genes aggregated across >500 cell types, generating 1,860 human genome… Show more

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Cited by 1 publication
(2 citation statements)
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“…There are clear shortcomings to this approach, as many enhancer targets are not the closest genes, leading to mis-assignments (e.g. 24,[25][26][27]. However, potentially more accurate methods for target-gene assignment rely on gene expression data, epigenetic data, and/or chromatin conformation data that are frequently not available for the species we are studying and thus difficult to incorporate into our prediction pipeline (27)(28)(29)(30).…”
Section: Post-processingmentioning
confidence: 99%
See 1 more Smart Citation
“…There are clear shortcomings to this approach, as many enhancer targets are not the closest genes, leading to mis-assignments (e.g. 24,[25][26][27]. However, potentially more accurate methods for target-gene assignment rely on gene expression data, epigenetic data, and/or chromatin conformation data that are frequently not available for the species we are studying and thus difficult to incorporate into our prediction pipeline (27)(28)(29)(30).…”
Section: Post-processingmentioning
confidence: 99%
“…24,[25][26][27]. However, potentially more accurate methods for target-gene assignment rely on gene expression data, epigenetic data, and/or chromatin conformation data that are frequently not available for the species we are studying and thus difficult to incorporate into our prediction pipeline (27)(28)(29)(30). Putative target genes are then mapped to their D. melanogaster orthologs (if an ortholog exists) using the Orthologer software from the Zdobnov lab (31) (see Methods).…”
Section: Post-processingmentioning
confidence: 99%