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Figure 1 | BMC Genomics

Figure 1

From: Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment

Figure 1

Composition-bias plots reveal systematic TF PFM nucleotide content bias in motif over-representation analysis. Foreground data was obtained from an E2F1 ChIP-Seq study and processed using the oPOSSUM TFBS over-representation analysis software. Each plot presents a motif over-representation score (y-axis) relative to the GC content of the PFMs (x-axis). The over-representation scores reflect the difference between the frequency of motifs in the foreground compared to a background (the background differs between panels). The names of the 5 top ranked PWMs are displayed on the plot. The dotted line at over-representation score 100 is an arbitrarily placed visual point of reference. The sequence logos represent the binding models for E2F1 and E2F4 respectively. (a) Background composed of randomly selected mappable genome sequences. (b) Background generated, using BiasAway, with a GC composition matched to the ChIP-Seq sequences and drawn from the set of mappable sequences.

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BMC Genomics

ISSN: 1471-2164

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