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Cell Regeneration
Figure 2 | Cell Regeneration

Figure 2

From: glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data

Figure 2

Example graphical output from glbase. Code and raw data can be found in the glbase directory (glbase/examples/). (A) Frequency of the STAT3 DNA-binding word (‘TTCnnnGAA’) in a list of STAT3 ChIP-seq binding sites, compared to a random selected background from the control ChIP-seq sample. (B) Heatmap of top 20 and bottom 20 up- and down-regulated transcription factors when macrophages are stimulated with IL-10. (C) Scatter plot of RNA-seq data (D) Genomic distribution of STAT3 binding in IL-10 stimulated macrophages. (E) Average phastCons evolutionary conservation score around a list of Sox2-Oct4 ChIP-seq binding peaks. (F) Heatmap of p300 recruitment in mouse ES cells for a list of Sox2-Oct4 ChIP-seq binding peaks. Raw data comes from the GEO accessions GSE31531 [14], the ENCODE project [16], GSE11431 [15] and the phastCons measure of evolutionary conservation [12]. Transcription factor annotation was based on the DNA-binding domain database [17].

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