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- W1969012014 abstract "Chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) has great potential for elucidating transcriptional networks, by measuring genome-wide binding of transcription factors (TFs) at high resolution. Despite the precision of these experiments, identification of genes directly regulated by a TF (target genes) is not trivial. Numerous target gene scoring methods have been used in the past. However, their suitability for the task and their performance remain unclear, because a thorough comparative assessment of these methods is still lacking. Here we present a systematic evaluation of computational methods for defining TF targets based on ChIP-seq data. We validated predictions based on 68 ChIP-seq studies using a wide range of genomic expression data and functional information. We demonstrate that peak-to-gene assignment is the most crucial step for correct target gene prediction and propose a parameter-free method performing most consistently across the evaluation tests." @default.
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- W1969012014 date "2013-11-21" @default.
- W1969012014 modified "2023-10-17" @default.
- W1969012014 title "Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data" @default.
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- W1969012014 doi "https://doi.org/10.1371/journal.pcbi.1003342" @default.
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