Help on expression data display

Gene expression data

Gene expression data display

Expression data displayed on this site have been imported from public data repositories such as GEO (NCBI) and ArrayExpress (EBI).

The data are grouped by experiments displayed in the following format:

Novel response to microtubule perturbation in meiosis
[PubMed] [Website] Design: compound treatment, growth condition, time series; Strain: SK1; Type: MATa/alpha

Display microarray expression data by clicking on the [Show all] link at the top of the list of studies, or the

icon before the title of the study.

Normalized expression signals for each matching probeset are then displayed in a bar chart as follows:

Novel response to microtubule perturbation in meiosis
[PubMed] [Website] Design: compound treatment, growth condition, time series; Strain: SK1; Type: MATa/alpha

Array YG_S98
Probeset 4558_at (16 matching probes out of 16) [Show linear scale][Show log2 scale]

"Percentiles" indicate the positions of the percentiles of all measurements in the experiment (percentiles divide an ordered set of values into 100 parts each of which contains one-hundredth of the total; the 50% percentile corresponds to the median).

The expression value for each sample condition is indicated by a colour-coded horizontal bar (colours depend on growth media, tissue, mating type, or sex as appropriate). If two or more replicates are available, the median value is displayed and the individual values are indicated as black vertical lines.

A dashed red line at an intensity value of 100 indicates a rough empirical background noise level (see also the section "Interpreting gene expression data" below).

Click on the sample condition name to call up the numeric intensity values and the Minimal Information About a Microarray Experiment (MIAME) annotation of the samples.

2 replicates
intensities 209.298, 155.584
Organism: Saccharomyces cerevisiae
Sex/Mating Type: MATa/alpha
Age Determination/Type: unknown
Organism Developmental Stage: meiotic development
Sample Material Type: whole organism
Strain/Line/Cultivar: SK1
Growth Conditions: YPD medium
temperature: 25 °C
media: YPD
Microarray data repository: GEO GSE1693

Interpreting gene expression data

Most probesets on an oligonucleotide array yield expression values greater than zero, even those for which the corresponding gene is not expressed. The presence of a signal by itself is not sufficient evidence to assert that a transcript is present in the sample.

The display provides several means to help determine the significance of a given measurement:

The dashed red line at intensity value 100: This indicates a rough empirical background noise level. Any signal below this range is too weak to be distinguished from noise using the microarray system. It may, however, still indicate biologically significant expression if other molecular or genetic evidence suggests the gene to be expressed.
The percentile range: Budding yeast expresses approximately 80-90% of its genes during mitotic growth in rich medium. Cells in higher eukaryotes express about 50% of the genes represented on arrays. This indicates that yeast signals falling below the 10-20th percentile and signals obtained with samples from higher eukaryotes (such as mammals) falling below the 50th percentile are within background noise.
The log2 scale: The base-2 logarithmic scale is used to better compare expression values across conditions. A change of one unit in the log2 scale indicates a twofold increase (a doubling) of the normalized linear value.
Measurements from replicates: Expression values from replicates help assess whether changes in expression signals are reproducible, thus significant. Variation of expression values across samples is an indication of the biological variation of expression level.

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