Contents
The presentation of gene expression data is aimed at better facilitating access to public microarray experiments. Researchers using SGD can retrieve mRNA expression data on their locus of interest, as well as other loci with similar expression levels.
The primary convention followed by the vast majority of microarray experiments is this:
Red means the mRNA level (expression) is increased, relative to the standard.
Black means the mRNA level (expression) is unchanged, relative to the standard.
Green means the mRNA level (expression) is decreased, relative to the standard.
Thus, the first feature displayed on the Locus' Expression page is a colorimetric scale bar, with which to determine the relative expression levels within the 2-color representation of the data.
Immediately below the scale bar is a table, the first row containing the locus whose expression information was requested initially. The following 19 rows contain those genes whose expression most highly correlates with the locus of interest.
The 2-color representation often does not offer enough differentiation between data points, especially at the spectrum's extremes. Therefore, below the table is a graph reflecting the numerical values for the locus of interest.
Clicking on the "Browse clustered data" link, opens a pop-up window containing the cluster browser.
- Internal Sets
- Diauxic Shift : identifies genes involved in the switch from anaerobic (fermentation) to aerobic (respiration) metabolism.
- DeRisi, J., et al. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686
- Sporulation : identifies genes whose mRNA levels are regulated by the sporulation, including meiosis and spore morphogenesis.
- Chu, S., et al. (1998). The transcriptional program of sporulation in budding yeast. Science 282(5389):699-705
- Alpha-factor concentration : monitors genes involved in the response to increasing levels of mating pheromone.
- Roberts, C., et al. (2000). Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles. Science 287(5454):873-880
- Alpha-factor time series : shows genes that demonstrate a temporal response to mating pheromone.
- Roberts, C., et al. (2000). Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles. Science 287(5454):873-880
- Histone depletion : indentifies genes whose transcriptional patterns are disrupted by depletion of histone H4
- Wyrick, et al. (1999). Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402(6760):418-421
- External Sets
- this document does not specifically address the sets below, as they have different interfaces.
- Cell Cycle : designed to identify all genes whose mRNA levels are regulated by the cell cycle.
- Site supplementing Spellman et al., (1998). Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Molecular Biology of the Cell 9, 3273-3297. Additional help for the cell cycle data set can be found here.
- Evolution under glucose limitation : designed to identify transcriptional differences between ancestors and evolved descendants after selective pressure (aerobic growth under glucose limitation).
- Site supplementing Ferea, T. L., et al. (1999). Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. 96(17):9721-9726. Additional help for the glucose limitation data set can be found here.
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