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Fig. 7 | Genome Biology

Fig. 7

From: GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

Fig. 7

GRiNCH applied to Hi-C datasets along developmental time courses. A Interaction profile near the Zfp608 gene in mouse embryonic stem cells (mESC), neural progenitors (NPC), and differentiated cortinal neurons (CN). Heatmaps are of Hi-C matrices after log2-transformation of interaction counts for better visualization. GRiNCH clusters are visualized as blocks of different colors under the heatmap of interaction counts. Genes in the nearby regions are marked by small boxes, and a heatmap of their corresponding RNA-seq levels (in log-transformed TPM) is shown underneath each gene. ChIP-seq signals from H3K27ac, H3K4me3, and CTCF are shown as separate tracks. B Interaction profile near Syap1 and Ap1s2 in mouse embryonic stem cells (mESC), neural progenitors (NPC), and differentiated cortinal neurons (CN). C Top 20 TFs from a collection of 746 TFs ranked based on their motif enrichment in GRiNCH TAD boundaries from the mouse reprogramming time course data. The significance of their fold enrichment was calculated with the hypergeometric test and TFs were ranked by descending negative log p-value

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Genome Biology

ISSN: 1474-760X

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