Fig. 7

Integrative multi-omics analysis of chromatin accessibility, epigenomic, and transcriptomic data from WT and Dido1ΔE16 cells identifies distinct molecular alterations in B cell differentiation. A. Genome browser snapshot of genomic regions identified in ATAC-seq, ChIP-seq, and RNA-seq data analysis. The ATAC-seq and RNA-seq tracks were obtained from male (n = 8) mouse samples of different ages. The ChIP-seq tracks were obtained from eight samples as described in Fig. 6A. The bottom inset of panel A displays the ATAC-seq, ChIP-seq, and RNA-seq signals on a randomly chosen genomic region (Chr19:52,980,000–53,250,000). The peak identifiers are identical to those found in Supplementary Files 1 and 2. The Y-axis values indicate the mean of normalized reads per 10 bp (normalized using BPM with bamCoverage of deepTools). B. Overlaps between gene lists from ATAC-seq, ChIP-seq, and RNA-seq experiments. C. Overlaps between genes sharing the same enriched ontology terms (i.e., GO Biological Processes, Molecular Functions or Cellular Components, KEGG Pathway, Reactome Gene Sets, WikiPathways). On the outside, each arc represents the identity of each gene list, using the same color code as indicated in the legend. On the inside, each arc represents a gene list, where each gene member of that list is assigned a spot on the arc. Dark orange color represents the genes that are shared by multiple lists and light orange color represents genes that are unique to that gene list. Purple lines link the same gene that are shared by multiple gene lists (notice a gene that appears in two gene lists will be mapped once onto each gene list, therefore, the two positions are purple linked). Blue lines link the genes, although different, fall under the same ontology term (the term has to be statistically significantly enriched and with size no larger than 100). The greater the number of purple links and the longer the dark orange arcs implies greater overlap among the input gene lists. Blue links indicate the amount of functional overlap among the input gene lists. D. Hierarchical cluster of enriched ontology terms. The heatmap cells are colored by their p-values; gray cells indicate the lack of enrichment for that term in the corresponding gene list