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iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
TLDR
We develop a computational method, called iRegulon, to reverse-engineer the transcriptional regulatory network underlying a co-expressed gene set using cis-regulatory sequence analysis. Expand
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Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state
Transcriptional reprogramming of proliferative melanoma cells into a phenotypically distinct invasive cell subpopulation is a critical event at the origin of metastatic spreading. Here we generateExpand
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Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic.
Transcription factors regulate their target genes by binding to regulatory regions in the genome. Although the binding preferences of TP53 are known, it remains unclear what distinguishes functionalExpand
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Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks
The identification of functional non-coding mutations is a key challenge in the field of genomics, where whole-genome re-sequencing can swiftly generate a set of all genomic variants in a sample,Expand
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Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models
TLDR
We trained Random Forest models for 45 cancer-related transcription factors, and used these to score variations in the HeLa genome and somatic mutations across more than five hundred cancer genomes. Expand
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Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks
The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based onExpand
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ACE-inhibition induces a cardioprotective transcriptional response in the metabolic syndrome heart
Cardiovascular disease associated with metabolic syndrome has a high prevalence, but the mechanistic basis of metabolic cardiomyopathy remains poorly understood. We characterised the cardiacExpand
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