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Illustration by Tasha Lewis In the chapter called "Sirens," whose motif is music, she recorded herself reading a sentence from the chapter, then cut a shape based on the sound wave of her voice out of a sheet of music.
The INOS for excluding a specific motif (G-ACA---TGT-C or TGAC/GTCA) is calculated from the sequence whose motif is replaced by random bases but with GC content of 42% as in the mouse genome.
The sequence motif associated with any given TF's direct DNA binding is somewhat predictive of its empirical occupancy, but a great deal of occupancy occurs at sites without the TF's motif, implying indirect recruitment by another TF whose motif is present.
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Alexis Mabille, whose motif was once a bow tie, had exchanged that for a new symbol: lacing up the leg of tight pants.
CCAAT/enhancer-binding protein α (CEBPα), whose motif was enriched in the neocortex dataset, and c-MYC, whose motif was enriched in the kidney dataset, regulate metabolic processes and would be reasonable candidate regulators of SIRT3.
Expression profiles of POU factors as well as of HMG and Forkhead factors whose motifs were also identified through promoter analysis led us to propose Oct4 (Pou5f1), Tcf7, Lef1, and Foxc1 as regulators of a transcriptional network potentially under control of Wnt signaling.
Column 5 lists Table 14 entries whose motifs are very similar (max. 1 mismatch).
Although some of these unassigned motifs may be artifacts, others may simply correspond to TFs whose motifs are not contained in the two motif databases we searched.
The large numbers of motifs discovered by DREME that can be reliably assigned to TFs suggests that unassigned motifs may represent binding by other TFs whose motifs are not yet known.
Figure 1C shows song motifs from two pupils, a repeater and a non-repeater, who learned their songs from the same tutor whose song motif is shown.
Interestingly, the retinoid heterodimer receptor (Fxr/Rxr) complex, whose binding motif is enriched in the promoters of the genes of the UGE+Sca-1Hi cluster (Table 2), is also implicated in the regulation of lipid metabolism [54].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com