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ARF6 DNA-binding affinity was based on the peak score from the ARF6 ChIP-Seq analysis with CSAR.
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The goal is to predict the peak scores from the peak vectors.
Analysis of the sequences from the top 40 peak scores from HLH-1 ChIP-chip revealed E-Box sequences (CANNTG) as the primary over represented sequence motif when the width interval was set to either six or eight nucleotides; 7 of the top 10 motifs were E-boxes (Figure 5A).
To identify these changes on all promoters, we subtracted the monocyte-specific peak scores from those identified in macrophages or DCs.
To further validate our ChIP-PCR findings, we also pursued ChIP-qPCR analyses of six gene promoters of interest with high peak scores from the RR gene list, and validated that Sox2 was significantly more frequently bound to these promoters in the RR cells when compared to the RU cells.
The resulting score (peak score) for each probe was the −log10 P-value from the windowed KS test around that probe.
Top-ranked 15 stem cell and/or cancer-associated genes of interest with >2.0 peak score derived from the MCF7 reporter responsive cells and their final adjusted microarray peak scores are summarized.
The absolute peak score occurs for substrings drawn from within the N-terminal 60 residues; 56 of the 58 most closely related homologous subsequences as scored by BLAST come from genomes that also encode the mycofactocin system.
The "true" peak score is the score provided by [9], and is derived from the frequency of reads of ChIP-Seq data.
Ledalab measures showed no significant difference from peak scoring in most contrasts.
The ICED is derived from the peak scores of the Index of Disease Severity and the Index of Physical Impairment using an algorithm specific to the ICED.
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