ENCODE’s various tests (gray boxes) translate DNA’s features into functional elements along a chromosome.

(Science. 2012 Sep 7;337(6099):1159, 1161)

MAKING A GENOME MANUAL

(Nature. 2012 Sep 6;489(7414):46-8)

Impact of selection on ENCODE functional elements in mammals and human populations

(10.1038/nature11247)

Interactions between TFs

(10.1101/gr.139105.112)

Cell-type–specific binding of sequence-specific and non-sequence-specific TFs

(10.1101/gr.139105.112)

Statistical significance of co-occurences of motif families

(10.1038/nature11232)

Quantifying transcription factor impact on chromatin accessibility

(10.1038/nature11232)

Transcription factor drivers of chromatin accessibility

(10.1038/nature11232)

A genome-wide map of distal DHS-to-promoter connectivity

(10.1038/nature11232)

General features of the DHS landscape

(10.1038/nature11232)

Identification and directional classification of novel promoters

(10.1038/nature11232)

Hypothetical model for establishment of enhancer chromatin states

(10.1074/jbc.R111.296491)

Distribution of looping interactions across cell types and their relationship with chromatin features and gene expression

(10.1038/nature11279)

Stereotyped regulation of chromatin accessibility

(10.1038/nature11232)

Comparison of the prediction accuracy of high- and low-CpG content promoter gene categories

(10.1186/gb-2012-13-9-r53)

Quantitative relationship between chromatin feature and expression

(10.1186/gb-2012-13-9-r53)

Genetic variation in regulatory DNA linked to mutation rate

(10.1038/nature11232)

Summary of pseudogene annotation and case studies

(10.1186/gb-2012-13-9-r51)

Modelling transcription levels from histone modification and transcription-factor-binding patterns

(10.1038/nature11247)

Integration of ENCODE data by genome-wide segmentation

(10.1038/nature11247)

High-resolution segmentation of ENCODE data by self-organizing maps (SOM)

(10.1038/nature11247)

CTCF in vivo binding exhibits widespread plasticity

Patterns and asymmetry of chromatin modification at transcription-factor-binding sites

(10.1038/nature11247)

Allele-specific ENCODEelements

(10.1038/nature11247)

Impact of DNA methylation on cell-selective CTCF binding

(10.1101/gr.136101.111)

Comparison of genome-wide-association-study-identified loci with ENCODE data

(10.1038/nature11247)

Using a self-organizing map to cluster DHSs by cross-cell-type pattern

(10.1038/nature11247)

Three-dimensional connections across the genome-Overall Network

(10.1038/nature11245)

Networks of looping interactions

(10.1038/nature11279)

Transcriptional regulatory circuitry of PPARGC1A and its network partners

(10.1101/gr.127761.111)

Transcription factor co-association

(10.1038/nature11245)

Novel mammalian conventional mirtrons

(10.1101/gr.133553.111)

Novel mammalian 5'-tailed mirtrons

(10.1101/gr.133553.111)

Comparison of read abundance from canonical miRNA loci and mirtrons

(10.1101/gr.133553.111)

Evolutionary conservation of lncRNAs

(10.1101/gr.132159.111)

Microarray analysis of lncRNA expression in the human body

(10.1101/gr.132159.111)

Genome-wide characterizations of regulatory regions

(10.1074/jbc.R112.365940)

SNPs discovered from ChIP-seq and disease-associated SNPs

(10.1186/1471-2156-13-46)

Examining ENCODE elements on a per individual basis in the normal and cancer genome.

(10.1038/nature11247)

Phenotype level overview of the overlap between associations and ChIP-seq binding

(10.1101/gr.136127.111)

Functional SNPs in linkage disequilibrium with an associated lead SNP

(10.1101/gr.136127.111)

Systems-level predictions

(10.1126/science.1227739)

（完）