Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

10 Characterization of network topology

ENCODE data analysis helps to describe the various types of regulatory "wiring" implicit in the genome

This is a preview of subscription content, access via your institution

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Transcription factor co-association.
Figure 2: Overall Network
Figure 4: Motif Analysis
Figure 2: Distribution of the six types of regions in the genome in K562.
Figure 4: Co-association between Transcription Factors.
Figure 4: Networks of looping interactions.
Figure 6: Transcriptional regulatory circuitry of PPARGC1A and its network partners.
Figure 5: A genome-wide map of distal DHS-to-promoter connectivity.
Supplementary Figure 13: Cell-type-specific enhancers at the IFNG locus.
Supplementary Figure 14: Interaction and GO class enrichments via signal-vector correlation.
Supplementary Figure 15: Statistical significance of co-occurences of motif families.
Figure 6: Stereotyped regulation of chromatin accessibility.
Supplementary Figure 16: Examples of stereotyped DNaseI patterns across cell lines.
Supplementary Figure 17: Top-ranked matches of stereotyped DNaseI patterns across cell lines.
Supplementary Figure 18: Using a self-organizing map to cluster DHSs by cross-cell-type pattern.
Supplementary Figure 19
Supplementary Figure 20: Instance counts of patterns discovered by the SOM (Supp. Fig. 18)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

10 Characterization of network topology. Nature (2019).

Download citation

  • Published:

  • DOI:


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing