Calcium-mediated changes in transcript abundance are enriched for functional gene categories. (a) Hierarchical clustering of the potassium chloride (KCl) transcript dataset identifies six major patterns of gene expression over the 24-hour time course. The number of transcripts contained in each cluster is designated in parentheses. Shown in each plot is the averaged expression behavior of all transcripts in the indicated cluster, with error bars indicating the deviation from the mean for the entire cluster. Expression behavior of each transcript was obtained by subtracting the mean of all points at all times from each expression value in the original time series, and dividing by the standard deviation. KCl-treated time points are indicated in blue. Thapsigargin (TPG) treatment is indicated in red. (b) Gene Ontology (GO) analyses of the transcripts in each cluster reveals functional enrichment in clusters T1 to T4. (c) Polymerase chain reaction performed on cDNA from treated and untreated IMR-32 cells validates changes in transcript abundance predicted by the microarray data. PREX1, a gene whose abundance was not predicted to change, served as a normalization control. (d) Transcripts regulated by KCl stimulation at 24 hours are similarly affected by TPG treatment. Numbers indicate upregulated and downregulated transcripts. Among those transcripts affected by both KCl and TPG, 116 were upregulated and 573 were downregulated. ARRDC3, arrestin domain containing 3; BNIP3, BCL2 adenovirus E1B 19 kDa interacting protein 3; ETV5, ets variant gene 5; GLI3, GLI-Kruppel family member 3; KCNK7, potassium channel, subfamily K, member 7; PREX1, phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1; OVGP1, oviductal glycoprotein 1; STC1, stanniocalcin 1; ZNF143, zinc finger protein 143.
McKee et al. Genome Biology 2007 8:R159 doi:10.1186/gb-2007-8-8-r159