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. 2008 Apr 25;9:214. doi: 10.1186/1471-2105-9-214

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Copyright © 2008 Daigle and Altman; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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YOR020C and YJR044C differential expression stories. Stories are shown for YOR020C alone (A) and YOR020C + YJR044C (B) from the hsf1 dataset. Gene names have been removed for clarity. Black arrows mark the two genes. Large clusters of genes represent individual upstream motifs. Sizes of red (boosted with respect to original rank) genes are directly proportional to magnitudes of M-BISON scores; sizes of blue (lowered with respect to original rank) genes are inversely proportional to score magnitudes. YOR020C is boosted in score by M-BISON, and it is clear that this is due to the many boosted genes surrounding it in knowledge. In contrast, YJR044C receives a lower score due to the motifs, in spite of many boosted genes surrounding it. By expanding the DE story in (B), the reason for this is revealed: YJR044C is connected through two additional motifs to 61 genes that are also lowered.