Figure 2

Searching for pairwise comparisons mapped to the Cell Ontology. A) Gene lists resulting from almost 8000 pairwise comparisons were mapped to the CL by creating terms (in green) that represent genes with 1.5 fold-higher or 1.5-fold-lower expression, between two cell types. These terms were mapped by creating has_genes_up_regulated_for (green R relation) and has_genes_down_regulated_for (red R relation) relationships. This structure allows for ontologically driven searches, depicted in text. B) Pairwise comparisons for genes up regulated in ‘germinal center B cell’ compared to all other mature B cells. Note how search finds the other B cell types by ‘Ancestor’ of ‘mature B cell’. C) Search strategy to find the 256 pairwise comparisons that exist between mature B cells and other types of mature lymphocytes. Note the third constraint that is added in the search to eliminate comparisons between types of mature B cells.