Most annotations of the functional DNA elements revealed by ENCODE follows an ontogenic vocabulary adapted to biomedical research, although the notion of functional DNA in ENCODE has been long debated [ 16, 17].
Only six of the 147 cell types looked at in ENCODE were studied in the amount of detail now possible.
We used Enrichr37 to examine enriched histone marks (Epigenomics Roadmap HM ChIP-seq) and transcription factor binding sites TFBS ENCODE_TF_ChIP-seq_20155) in ENCODE human cell lines based on the program Enrichr.
Notably, combinations of these assays have been widely used in ENCODE and modENCODE projects for genome-wide identification of functional elements involved in gene regulation in model organisms17,18.
Four schizophrenia-associated pathways 'potassium ion transport', 'regulation of heart contraction', 'voltage gated potassium channel complex', and 'potassium channel activity' were enriched in ENCODE FARE track "wgEncodeOpenChromFaireMedulloPk" (a cell line of brain, as shown in Table S5), indicating many SNPs in these pathways may regulate the gene expression in brain.
CNC10 maps upstream of PSMG1 and BRDW1 genes in ENCODE region ENr133.
To determine the overall expression status of genes in ENCODE regions based on Affymetrix, Sanger ENCODE array and Illumina analysis, expression levels of 618 annotated genes were binned into quartiles based on RMA (Affymetrix) or Z-scores (Sanger ENCODE arrays).
We used the 438 promoters and 464 enhancers that Won et al. reported in ENCODE region as additional filters to remove false positives of cis-module predictions and identify functional sites in the HeLa cell.
This nucleosomal exon bias was seen for the set of expressed genes in ENCODE regions which we had analyzed by ChIP-chip, alsoalso genome-wide for all expressed genes in K562.
Chromatin categories as in ENCODE project.
4. "highly expressed in ENCODE, but hardly expressed in PH".
