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10 Characterization of network topology

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

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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)

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10 Characterization of network topology. Nature (2019). https://doi.org/10.1038/nature28179

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