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Figure 6 | BMC Genomics

Figure 6

From: Cell-type specificity of ChIP-predicted transcription factor binding sites

Figure 6

Genotype differences in sequence motifs can give cell-type specific peaks. A) A specific example of how different alleles can create differences in sequence motifs, possibly causing cell-type specific TF-binding. SNP rs7138374 (chr12:130,642,970) is located at the highly conserved position 7 in the highest scoring AP-1 sequence motif in a K562-specific c-Fos peak region. K562 is homozygous for the A allele (green letter) and has a peak (illustrated here by a curve; top of panel). HeLa-S3 is homozygous for the T allele (red letter), which disrupts the motif, and has no peak (illustrated by absence of curve; middle of panel). The bottom part of the panel shows the sequence logo for the AP-1 sequence motif. B) A comparison of PWM motif score distributions in K562- and HeLa-S3-specific peaks that contain SNPs in the highest-scoring sequence motif regions in the peaks, and where these SNPs are homozygous but have different alleles in the two cell types. The two leftmost box-plots compare for the K562-specific peaks that contain such homozygous SNPs, the PWM motif scores for the K562 and HeLa-S3 genotypes (K562/K562 and K562/HeLa, respectively); the two rightmost box-plots compare for the HeLa-S3-specific peaks that contain such homozygous SNPs, the motif scores for the HeLa-S3 and K562 genotypes (HeLa/HeLa and HeLa/K562, respectively). The K562-specific peaks have significantly higher motif scores for the K562 genotype (K562/K562) than for the HeLa-S3 genotype (K562/HeLa), whereas the HeLa-S3-specific peaks have significantly higher motif scores for the HeLa-S3 genotype (HeLa/HeLa) than for the K562 genotype (HeLa/K562; p = 1.910−4and p = 1.110−5, one-sided paired t-tests for K562- and HeLa-specific peaks, respectively).

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