Additional file 6.
Analysis of genes within the Top 500 with increased H3K4me3 which did not meet significance criteriae for increased gene expression. (A) Categories of genes which failed to reach the significance criteriae (>2-fold increase, p<0.05) for increased gene expression. (B) Details of gene expression analysis  and epigenetic profile (bottom) for SOX5 as an example of a chondrogenic signature gene with <2-fold, but significantly changed mRNA expression. (C) ChIP-seq signal tracks for histone modifications of the SOX5 gene. Exon-intron structures and coding strand direction are depicted on top. UCSC Genome Browser. (D) ChIP-seq signal tracks of KLHL5 as an example for genes within the top 500 genes with increased H3K4me3 due to activation of an alternative promoter, without change in the level of mRNA expression. (E) Example of wrong gene annotation. ChIP-seq signal tracks for histone modifications and data for changes in gene expression for RAB4B and MIA.
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Herlofsen et al. BMC Genomics 2013 14:105 doi:10.1186/1471-2164-14-105