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Fig. 3 | Genome Biology

Fig. 3

From: Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors

Fig. 3

Identification of heterotypic TF co-localization groups. a Co-localization enrichment between different TFs in human GM12878 cells. CE values between different lymphoblastoid TF pairs are shown as a color matrix. Colors indicate CE value, where red or blue represents higher or lower than expected contact frequency respectively. Ward’s method [79], using the distance measure in Eq. 5, was used to define row and column orders. Alternative clustering, using Euclidean distances with Wards’ method, is shown in Additional file 2: Figure S4a. The two major sub-network groups that become apparent are labelled at the left. b Co-localization enrichment between different TFs in mESC genome structures. Structural proximity enrichment (PE) values between the different mESC TF pairs are shown as a color matrix. Colors indicate PE values; enrichment/depletion of spatially co-localized binding sites compared to the random expectation, where red or blue represents higher or lower than expected co-localization respectively. Data is shown for the six best-defined structures in Stevens et al. [36] combined. Row and column order was determined by using hierarchical clustering based on Wards’ method. The two major sub-network groups that become apparent are labelled at the left. c 3D genome distributions of group 1/2 TF sites. Locations of TF binding sites in group 1 and group 2 are shown as purple and green circles respectively and superimposed upon a thin section of a whole genome structure (left). The same view is also shown with the A and B chromosome compartments colored red and blue respectively (right). The data shown is “Cell1” from Stevens et al. [36]; modelled at 100-kb particle resolution using single-cell Hi-C contacts from mESCs. d 3D distributions of group 1/2 sites in Chr4 and Chr9. Chromosomes 4 and 9 shown in isolation, taken from the structure shown in c. TF binding sites in the group 1 and group 2 groups are shown as green and purple circles respectively

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