Figure 1.

Distributions of hybridization values for probe sets. Each histogram depicts the number of replicates (from a total of 241) with a given hybridization value for a given probe set. For illustrative purposes, we display the distribution of hybridization values of three probe sets selected using the gap method as markers corresponding to (a) a known neural stem cell marker (Nestin; probe set 1449022_at), (b) a novel stem cell marker encoding a protein of known function (phospholipase Pla2g7; probe set 1430700_a_at) that we observed to be upregulated in bone marrow mast cell precursors and in undifferentiated mammospheres, and (c) a novel stem cell marker corresponding to an uncharacterized transcript upregulated in undifferentiated V6.5 and J1 murine embryonic stem cells (2410146L05Rik; probe set 1460471_at). Details on these three cases can be obtained through our online webserver [21] by viewing group numbers 73, 497, and 265, respectively. (d) For comparison, we show the distribution for a housekeeping gene (Eef1a1; probe set 1424635_at), a ribosomal translation elongation factor protein, which is always expressed and was not classified as a marker in our analysis. For robustness, the segregation of the samples (indicated by red and blue bars in the three marker distributions for the down and upregulated groups, respectively) is derived by analysis of the global set of patterns (see Materials and methods) and might not correspond perfectly to the distribution observed here. See, for example, a single replicate in the distribution of Nestin, which is left of the gap in the distribution but was (correctly) associated to the upregulated (blue) group.