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Here TFs with less than five probes overlapped between the binding data and the histone modification data were excluded.
Histone modification data were taken from ChromatinDB [ 11], a database of genome-wide histone modification patterns for Saccharomyces cerevisiae.
So far, lots of genome-wide histone modification data were generated in mouse and human ES cells.
Histone modification data were taken from ChromationDB [ 33], a database of genome-wide histone modification patterns for Saccharomyces cerevisiae.
Protein modification data were then used in conjunction with results from gene expression studies to generate hypotheses on the signaling processes affected by HNE and the resulting cellular consequences.
The proportion of ECRs associated with H3K4me1 may be lower for fish because histone modification data were obtained only from whole embryos at 24 h post fertilization (hpf), rather than from multiple tissues and developmental time points as for the mouse.
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Chromatin modification data was used to predict the functional sites and to further remove false positives.
Histone modification data is quite useful compared to conservation studies because histone modifications strongly correlate with specific biological activities.
The chromatin modification data was obtained from [ 23, 17].
Therefore, approaches that integrate expression and histone modification data are essential to curate transcription units.
However, simpler models, for instance, predicting gene expression from histone modification data are already very useful.
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