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Functional transcription factor binding motifs have a strong location bias towards the transcription start sites of human and mouse genes
Yuval Tabach
Weizmann Institute of Science, Israel

We present a novel way of finding functional transcription-factor binding-sites, allowing a "flexible" threshold and considering location bias and GC content. We perform a comprehensive analysis of 134 biological groups and 412 motifs. Supported with experimental evidence we show that generally, binding-sites located 200bp upstream to the TSS are functional.

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Detecting cis-regulatory motifs for cooperatively binding proteins
Liesbeth van Oeffelen, Yves Moreau, Bart De Moor
KU Leuven, Belgium

To find regulatory motifs in DNA, one usually determines a position weight matrix (PWM) based on observed binding sequences and predicts regulatory motifs by scoring the upstream region of each gene. However, this method assumes that only one protein copy is involved, and adaptations are required for cooperatively binding proteins.

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