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Motif analysis for

Exhaustive motif analysis for the first time revealed unique sequence features of eRNAs.

We combined BLAST search methods and motif analysis for use in elucidating the relationship between gene function and evolution.

Many existing work depends on a secondary step of sequence motif analysis for locating binding sites in detected binding regions.

We analyzed the roles of these two transcription factors in regulating transcription using ChIP-seq data for NFIB, and RNA expression data and motif analysis for both.

The splicing motif analysis for the complete set of AS genes for chicken, human and mouse genomes yielded consistent values in the three genomes.

(E and F ) Motif analysis of BQS for K562 for 3- and 4-gene motifs, using the same convention as described in Figure 5. (G ) Genes implicated in the formation of long feedback loops in K562 are reported with the number and percentage of loop created, the length of the longest incomplete feedback loops involving the gene in GM12878 are also indicated.

Results for DNA regulatory motif analysis of human orthologs for the stimulated gene groups provided evidence for 51 putative NF κB targets in the Early group and 145 in the Late group.

(C and D ) Motif analysis of BQS for 3- and 4-gene motifs, using the same convention as described in Figure 5. (E ) Percentage of TFs which do not regulate other TFs compared to the corresponding random network.

(B, D and F ) Motif analysis of BQS for 4-gene motifs, using the same convention as described in Figure 5. (G ) Probability of creating additional long feedback loops by the addition of a random link between TFs in the GRN of dendritic cells at different times after a stimulus and the corresponding random network.

To further confirm the association with SCL/TAL1 and FLI1 with different sequences, we performed an unbiased motif analysis of binding sites for each factor unique for HE−DOX and HE+DOX.