ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

By Z. Ouyang, Qing Zhou, Wing Hung Wong. Proceedings of the National Academy of Sciences of the United States of America, 2009

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How researchers see this paper

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Machine learning in genetics and genomics (2015, methodology): “Some techniques aim to predict the expression of a gene on the basis of the DNA sequence alone 10 , whereas others take into account ChIP–seq profiles of histone modification 11 or transcription factor binding 12 at the gene promoter region.”
From RNA-seq reads to differential expression results (2010, background): “A few reports of these ‘integrative’ analyses have emerged recently [71-73].”
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer (2011, methodology): “The peaks called from MACS were used to construct a transcription factor association strength (TFAS) for each gene (Ouyang et al, 2009).”