Pipeline output for FOXA factor group, an example that highlights different aspects of the resource (in the interest of space, only selected columns are shown in the enlargements). (
a) The known and discovered motifs for the factor group, drawn with WebLogo (). Because the original orientation is arbitrary, motifs are flipped as necessary to increase the similarity of the displayed orientations. (
b and
c) Similarity between the motifs for this factor group and the motifs: (b) for this factor group, (c) for all other motifs that match at least one motif for this factor group with similarity

. Motif similarities are shown in black/white scale with gray starting at 0.65. (
d) Enrichments of motifs in the data sets for this factor group. Data sets are named indicating the factor, cell type/stage, lab code, followed by values to differentiate data sets and make them unique. Red is used for enrichment, blue is used for depletion (which is rare in this study). Enrichments are not shown for motifs when control motifs could not be generated or there was not sufficient information content to match at a
P-value. (
e) Magnified enrichment heatmap value. The three triangles represent the background regions used for enrichment; the top triangle is all regions, the left triangle is those within 2 kb of an annotated TSS and the right triangle is those outside the 2 kb window (the regions used in the left and right triangles partition that of the top triangle). The number shown is the enrichment in the inclusive background. Here we see an apparent contradiction: a higher enrichment for the union than the parts. This occurs because the higher counts permit a smaller confidence interval around the ratios used to compute the enrichment. Heatmaps are ordered using hierarchical clustering followed by optimal leaf ordering (). The Supplementary Results include an analysis of the robustness of the motif similarity metric and the enrichment values.