Finally, the third score (Sm) is the number of occurrences at that position divided by the total number of motif predictions, used to penalize matrices that are very noisy and occur at a very high frequency, which is often due to low specificity of the matrix.
Previously, a cis-motif-based prediction using 12 stress-responsive cis-motifs suggested that out of 83 soybean TCS genes, 30 genes might be dehydration responsive because these genes were found to contain dehydration-responsive ABRE and/or MYBR and/or MYCR motifs in their promoter regions.
We also evaluated the complementary strategy of identifying TF motifs overrepresented in the training CRMs, using a collection of known motifs for Drosophila, followed by motif-based CRM prediction using HMM models (Frith et al. 2003; Sinha et al. 2003).
Here, we report on GimmeMotifs, a motif prediction pipeline using a ensemble of existing computational tools (Supplementary Fig. S1).
Through a separate binding motif prediction analysis using JASPAR and PSCAN, we confirmed the STAT3 prediction based on enrichment of STAT3 binding sequences in DE genes at the late time points (Table 3).
The putative motif from genome-wide prediction using FIMO was found in the promoters of known targets, metH and leuA.
In order to test the feasibility of using the human genome as a reference set for motif prediction, we used a set of bovine and human expression data from cardiac tissue.
Site prediction using the Eukaryotic Linear Motif (ELM) resource confirmed that the second and third motifs of the 006/EB-MMG isoform are likely to constitute EB1 binding sites.
For motif prediction, we used the following three prediction programs: WeederTFBS 1.4.2 [ 60], MotifSampler 3a [ 61, 62] and PhyloCon 3.2 [ 63].
For de novo motif prediction, we used 1463 common binding regions of human CREB ChIP-chip and GABPα ChIP-seq data.
