TSS TSS 3'-terminus 3'-terminus

Upstream Downstream Upstream Downstream

Fig. 2. Pictorial representation of the cis region definitions used in BEARR. Traditionally, only upstream regions of the transcription start sites (TSS) are considered cis-regulatory regions, but discovery of functional binding sites within introns or around the 3' terminus have dispelled that restrictive definition. BEARR supports automatic extraction of up/downstream regions around TSS and the 3' end.

The second type of investigation concerns more the question of what might regulate a given set of genes. Here, a much smaller set of genes than that of the above framework is usually involved, and usually users possess a list of potential transcription factors of the gene set and their corresponding binding site motifs.

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