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Publication for EpiGRAPH
DNA methylation signatures link prenatal famine exposure to growth and metabolism
[…] enhancers. We then further characterized the P-DMRs by several enrichment tests, contrasting the 181 P-DMRs against the non-significant regions in the five associated annotations. First, we employed EpiGRAPH, a software for testing the co-occurrence of genomic regions with particular histone marks in public data sets. The 181 P-DMRs showed an increased co-occurrence with histone marks associated […]
High Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells
[…] ribed . Distribution of peak regions relative to gene regions was analyzed by CEAS . Top 10% of enriched regions for each ChIP-seq library were selected to identify the overrepresented features using EpiGRAPH (http://epigraph.mpi-inf.mpg.de/WebGRAPH/) . 2214 H1d/H1c common peaks, 1939 H1d unique peaks, 433 H1c unique peaks, 1891 H3K9me3 peaks, 4778 H3K27me3 peaks, and 3446 H3K4me3 peaks were analy […]
Extensive and coordinated transcription of noncoding RNAs within cell cycle promoters
[…] bridization to our custom tiling array (ChIP-chip). This analysis confirmed that the chromatin state at a majority of the newly defined transcripts was enriched in both H3K4me3 and H3K36me3 (). Using EpiGRAPH analysis to query our transcripts against approximately 900 published genomic attributes, the 216 putative transcribed regions are enriched for H3K4me3 (p<10−9) and RNA polymerase II binding […]
Inter individual variation of DNA methylation and its implications for large scale epigenome mapping
[…] s with high values exhibit inter-individually similar DNA methylation patterns while amplicons with low values do not (but may still exhibit similar average methylation levels across individuals).The EpiGRAPH web service (http://epigraph.mpi-inf.mpg.de/WebGRAPH/) was used to test a large number of genomic attributes for their ability to distinguish between amplicons with high versus low high-resol […]
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