Search: Chromatin motif database searching.
   Genome-wide: Genome-wide chromatin motif table.
   Genic: Genic chromatin motif table.
   Intergenic: Intergenic chromatin motif table.

 

Overview of the algorithm. (A) To identify accessible and inaccessible chromatin regions, we mapped FAIRE-seq reads to a diploid genome (GM12878) using Bowtie with the perfect match alignment. (B) We identified Differentiated Chromatin-State Regions (DCSRs) and then separated DCSRs into accessible and inaccessible chromatin groups. (C) To discover chromatin motifs, we used all combinations of DNA sequences with lengths ranging from 6 to 10 bases (motif candidates) to scan all of 41-base DCSRs. Given a motif candidate, we calculated frequency among all sliding windows for each DCSR, and then we perform paired t-test between frequency vectors of inaccessible chromatin group and accessible chromatin group. We selected chromatin motifs with P value < 0.01 in the paired t-test. (D) To annotate the motifs, we used the motif sequences and then performed BLAST alignment against all of transcription factor binding site sequences in both TFe and hPDI database. For each motif, we annotated the motif by the best E-value of alignment with homology > 0.8. (E) To provide the accurate annotation, we filtered out the transcript factors that are not expressed (FPKM < 1) by the RNA-seq data (SRP007417).