Figure 1

Changes in gene expression in human mast cells stimulated via the FcεRI (A) Clustering of 2,478 genes that exhibited a 2–200 fold change in expression over baseline "0" levels in two human umbilical cord blood-derived mast cell populations (> 99% purity) that were stimulated via the FcεRI (with anti-IgE at 10 μg/ml) for 1 or 2 h. The microarrays were scanned on a GenePix 4000 microarray scanner (Axon Instruments, Foster City, CA) and analyzed using Scan Alyze (M. Eisen; http://rana.stanford.edu/software/) or GENEPIX PRO (Axon Instruments). Single spots or areas of the array with obvious blemishes were flagged and excluded from subsequent analyses. All non-flagged array elements for which the fluorescent intensity in each channel was greater than 1.4 times the local background were considered well measured. A set of clones that consistently behaved poorly across arrays (time course) was identified and excluded from all analyses. The ratio values (experimental vs. reference) were normalized according to the baseline (time 0) value of each donor (so that the level of baseline mRNA expression would appear black in our color scale) and log-transformed (base 2). Hierarchical clustering was applied using Cluster (M. Eisen; http://rana.stanford.edu/software/). Genes were selected for this analysis if their expression level deviated from that in the unstimulated (time 0) mast cells by at least a factor 2 in at least 1 time point. The values from two experiments from two different donors (Donor 1 and 2) were analyzed simultaneously. The results were displayed with Tree View (M. Eisen; http://rana.stanford.edu/software/). Changes in gene expression were depicted according to the color scale shown at the bottom. The results are displayed in a table format, in which each row represents a series of measurements of mRNA levels for a single gene, and each column represents the measured mRNA levels for all of the genes in a single sample of cells. Each cell is colored to reflect expression of the corresponding gene in a specific cell sample, relative to its expression level prior to treatment with anti-IgE. Green color represents decreased expression; red color represents increased expression. As indicated, the scale extends from ratios of 0.125 to 8 (-3 to 3 in log base 2 units). Gray cells in the table indicate missing or excluded data. Genes for (B) cytokines, (C) chemokines, (D) molecules that can regulate potential interactions with T cells, B cells, or dendritic cells, and (E) adhesion molecules whose expression changed significantly (same populations as in (A)). ^* = Expression (or † = change in expression after FcεRI dependent stimulation) not previously reported for either human or rodent mast cells; ‡ = expression not previously reported for human mast cells.