Integration of high-throughput DNA binding and gene expression data to understand B cell development

Mark Maienschein-Cline, University of Chicago

Photo of Mark Maienschein-Cline

The differentiation of activated B cells into plasma cells and germinal centers is an important step in immune response to pathogens. This process has been shown to be highly dependent on the transcription factor Irf4, which we examine along with transcription factors Irf8 and PU.1. We use a combination of structural protein-DNA binding data, obtained by ChIP-seq experiment, and functional gene expression data, obtained by DNA microarray. Both methods produce tens of thousands to millions of lines of data per experiment, and informatic data analysis can be used to infer relationships between the different parts of the gene regulatory network represented in the experiments. By combining inferences across experiment types, we can recover the function of the transcription factors in B cell differentiation.

Abstract Author(s): Mark Maienschein-Cline, Aaron Dinner, Roger Sciammas, Harinder Singh