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Fig. 2 | Clinical Epigenetics

Fig. 2

From: CTCF loss mediates unique DNA hypermethylation landscapes in human cancers

Fig. 2

Transcriptional profiling of genes altered with CTCF knockdown. a Heat map of differentially expressed (DE) transcripts following 5 days of CTCF shRNA induction (Dox) versus uninduced vehicle control (vehicle). CTCF knockdown in HPECE6/E7 leads to 1308 significantly altered gene transcripts (FDR < 0.1). b Gene ontology (GO) analysis of DE genes, pathways with FDR q-value < 0.05. c Prostate cell CTCF binding sites (LNCaP ChIP-Seq) are enriched near transcription start sites (TSS) of DE genes identified after CTCF knockdown (P = 0.0001, Chi-square test for + 2 kb from TSS). d Venn diagram displaying overlap between differentially methylated genes and differentially expressed genes identified by arrays. Detected DMRs found within a promoter or transcribed region represented 3650 genes. Compared with 865 genes (865 genes from 1308 transcripts with gene annotation data), 249 genes were differentially expressed and contained a DMR (P = 1.1e−5; hypergeometric test)

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