c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression

BMC Bioinformatics

Table 1 Summary of results comparing c-REDUCE and f-REDUCE oligo predictions for ChIP-chip yeast data (part 1).

The 37 transcription factor (TF) motifs not discovered by the methods applied in [20] are listed in Tables 1 and 2. Only exact matches to the motifs (see Methods) are considered. The first and second columns list the transcription factor and known motif given in the Supplementary Table 3 file from [20]. The third column lists the environmental conditions examined (YPD: Rich medium, HEAT: Elevated temperature, SM: Amino acid starvation, H2O2Hi: Highly hyperoxic, H2O2Lo: Moderately hyperoxic, BUT14: Filamentation inducing, RAPA: Nutrient deprived and GAL: Galatose medium). The fourth and fifth columns list the results for c-REDUCE and f-REDUCE respectively. For example, "1: ATTGGY 3.0" for HAP2, indicates that the oligo ATTGGY was the first predicted oligo with a -log₁₀(p-value) of 3.0 under the YPD condition. The degenerate symbols are R = (A, G), Y = (C, T), M = (A, C), K = (G, T), S = (C, G), W = (A, T), B = (C, G, T), D = (A, G, T), H = (A, C, T), V = (A, C, G) and N = (A, C, G, T).

ISSN: 1471-2105