Figure 2

Gene expression profiles of T1 immature and mature B lymphocytes in response to BCR triggering. (A) k-means clustering using standard correlations was applied at several k values to classify all 2,454 genes (represented by 3,505 probes on the array) that showed differential expression between any sets of samples (see the key on the right). As shown in Additional file 5A, the result is independent of the selected k value. Shown are the clusters generated by running the analysis at k = 15. The cluster highlighted in red consists of Ptger4, Marcksl1, Myc, Crsp9, Ifrd1 and Pdhx. Data are means of normalized values of at least five microarray experiments. Note that the data from two different probes each (a, b) for Marcksl1 and Myc were used for clustering. (B) Transcription factor (TF) binding sites that are common to six promoter regions from the selected cluster of genes. A graphical representation of the matches shows the location for each binding site recognized by either the ETS family of TFs or Pax5 relative to the predicted transcription initiation sites (red arrows). As Pdhx was not validated by qPCR, it was excluded from the analysis. Note that we included two known promoter regions for Ptger4. Crsp9 is also known as Med7. The analysis was performed using the Genomatix software http://www.genomatix.de/. Only antibody producing cell-specific binding sites were analyzed. The statistics regarding the occurrence of these binding sites are provided in Additional file 5B.