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Pipeline publication

[…] intrinsic DNA binding properties of c-Myb has been extensively studied in vitro. Noteworthy, c-Myb binds to DNA in a two-step process—first the rapid formation of an unstable complex, followed by a slower transition to a stable complex, a process coupled with a conformational change in its DBD [,]. Therefore, c-Myb is expected to be able to bind more stably to chromatin than normal “tread milling” TFs. How this process is dependent on the DNA sequence in the factor-binding site remains to be elucidated., Several methods for prediction of TF binding using DGF have been described in different cell-types from yeast to human [–,–]. Different computational prediction tools such as Wellington [], CENTIPEDE [], DNase2TF [] and Footprint detection software [] are available. We have devised an approach that uses DGF datasets from [], in combination with MotifLab [] and four c-Myb motifs from the TRANSFAC database [] and weighted conservation using mammalian phastCons elements []. Our choice of conservation can be debated as regulatory elements may not necessarily be conserved across mammalian species []. A recent study showed that only about 22% of mouse TF footprints are conserved in human []. Even though several approaches have successfully identified active conserved regulatory regions across vertebrate species [–], many enhancers are poorly conserved and have species-specific TF binding [,]. Therefore, we cannot exclude the possibility that our filters will to a certain degree underestimate c-Myb binding sites in the six human cell-type […]

Pipeline specifications

Software tools CENTIPEDE, DNase2TF, MotifLab