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. 2019 May;29(5):857–869. doi: 10.1101/gr.243725.118

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© 2019 Sinnamon et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 4. — Cis-coaccessibility analysis using Cicero. (A) Cicero links at several coaccessibility score thresholds are heavily enriched for links that contain peaks present in the same topological associated domain (TAD) as determined by Hi-C methods (Dixon et al. 2012). The enrichment decreases at greater distances (x-axis). (B) t-SNE projection of cis-coaccessibility networks (CCANs) colored by the cell type with the greatest accessibility for the CCAN. Each point represents an individual CCAN. Networks generally group by cell type. CCAN 174, which includes the Prox1 gene shown below in D, is indicated with an arrow. (C) Accessibility Z-scores for CCANs for granule cells and microglia. (D) CCAN ID 174 including the Prox1 promoter (dentate granule marker gene). (E) CCAN 174 has the greatest accessibility signal in cells identified as dentate granule cells.