VISION-Index-Set
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README.md
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README.md

Snapshot

Epigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose a significant challenge for biologists to identify the regulatory events controlling each stage of cell differentiation. Here, we present a model-free method, called Snapshot, that uses epigenetic data to generate a hierarchical visualization for the DNA regions segregating with respect to chromatin state along any given cell differentiation hierarchy of interest. Different cell type hierarchies may be used to highlight the epigenetic history specific to particular lineages of cell differentiation. We demonstrate the utility of Snapshot using data from the VISION project, an international project for ValIdated Systematic IntegratiON of epigenomic data in mouse and human hematopoiesis.

Download index-set figures and bed files:

(https://github.com/guanjue/vision_index_set/blob/master/index_set_results.md)

Example of Snapshot output:

The data visualization for index-set-149 and corresponding GO analysis and MEME-ChIP TF binding motif analysis. (a) The hematopoietic cell differentiation tree colored by the average ATAC-seq signal in each cell type of the index-set-149. The violin plot represents the distribution of ATAC-seq signal in each cell type of the index-set-149 is in below. (b) The same cell differentiation tree colored by the most frequent functional annotation in each cell type of the index-set-149. The two most frequence functional annotation in erythroblasts lineage. The bar plot based on the proportion of each functional annotation in each cell type of the index-set-149 is below the cell differentiation tree. (c) The index-set-149 relevant GO term. (d) The index-set-149 significantly enriched TF binding motif from MEME-ChIP analysis.