Figure 1

Gene expression correlation analyses identify transcriptional regulators in the endomembrane system. Analyses are based on 1,517 sets of publicly available mouse microarray expression profiles (Affymetrix Mouse_430_2 arrays) that were processed as described in Methods [37]. (A) Pearson correlations were calculated between 19 cholesterol biosynthesis reference genes and a list of 1,683 known transcription factors [6, 38, 39]. Average correlation coefficients were calculated for each transcription factor. (B) Average correlations across datasets were calculated among a list of 778 ER-specific genes (Additional file 2). Hierarchical clustering was performed and the resulting dendrogram split into 6 clusters (Additional file 3). The cluster with the largest average, consisting of 97 ER genes, was then used to calculate correlations with known transcription factors as in (a). (A,B) Prior to calculating correlations with transcription factors, datasets were filtered to exclude those with an average coefficient of variation of less than 30% for the respective reference set such that only the indicated number n of data series were included for final analyses. Each plot shows the results for the 10 highest-ranking transcription factors; only DNA-binding proteins (GO:0003677) are shown. Complete results are given in Additional file 1.