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PlantIGB - Tiling array data

Numbers and base pairs - tiling array data and "graphs"

IGB can display positional, numerical data in the form of graphs, where the x-axis is the sequence and the y-axis represents numerical data, like probe intensity values.

To load data from the Arabidopsis genome tiling arrays described in Yamada, et al "Empirical analysis of transcriptional activity in the Arabidopsis Genome," appearing in Science in October, 2003, first look at the contents of this Web directory. The files in this directory contain expression data from several different tissues and from the forward (Watson) and reverse (Crick) strands of the target chromosomes.

To open the a file, download it to your local computer's hard drive. Click on the chromosome corresponding to the graph data file, and then use the File->Open menu to read the graph into IGB.

About the graph (expression) data files from Yamada, et al

To get detailed information about how these data were generated, i.e., information about image scanning, normalization, and other pre- and post-processing steps, the best source is the Science paper's supplementary data files. You can obtain these by visiting the on-line version of the article. We are grateful to Joe Ecker and his group, especially Huaming Chen, for sharing the data, answering our questions, and helping us use it to demonstrate IGB functionality.

To get started working with this data, you need to know three basic things about how the experiments were done as well as how to view the data in IGB.

  1. Data file names containing a "C" indicate that the data are from probes selected from the Crick (reverse or bottom) strand of the chromsome. Conversely, data files names containing a "W" are from the Watson (forward or top) strand.
  2. The target or sample preparation protocol used was the same as the target preparation protocol used with regular Affymetrix chips. This means that labeled cRNA is from the antisense strand of the target mRNA. Thus, Crick strand probes will hybridize to mRNAs expressed from bottom strand genes in IGB, and Watson strand probes will hybridize to mRNAs expressed from the top strand genes.
  3. Third, when you open a graph file, make sure you are showing the same chromosome that the graph is from.

File name conventions

Data files are named after the target chromosome, the sample, and the target strand:

[chromosome].[sample].[strand].gr.gz

The files are also compressed. (You don't have to uncompress them before opening them in IGB.)

Sample types include:

Graph view settings

To adjust how the graph looks, use the Graph Adjuster tab. This tab contains many functions useful for statistical manipulation of expression data within the viewer. For more information about IGB's statistical capabilities, read the IGB User's Guide sections related to displaying and manipulating graphs.

Once you open a graph file, it may be placed into a separate tier, or layer, in the main map window. (The default behavior may depend on IGB's default settings -- see the User's Guide for details.)

To compare it to known annotations and find expressed genes, it is helpful to be able to drag it over the tier of annotations you would like to examine. To turn the graph tier into a draggable graph, click the graph to select it and then click the Graph Adjuster tab. Then click the Floating checkbox. To see a vertical scale showing the range of values in the graph, click Y axis checkbox in the Advanced section.

It is also helpful to adjust the scale of values the graph shows. Expression values are usually very unevenly distributed. That is, there are a few values that are very large and many values that are much smaller. If IGB must show the entire range of values in the graph, it will be hard to see expression values in the lower ranges. The extremely large values are outliers and are (usually) not very interesting; to view a more informative range of values, use the Y-axis Scale box to adjust the visible range. To adjust the visible range, click the graph to select it and then click-drag the sliders or just type in new Min and Max values. boxes. This will have the effect of changing how large and small values are shown. For instance, if you set the Min and Max values to the 15th and 90th percentiles, then all values below and above these thresholds will be shown at the minimum and maximum heights (or color intensities) in the graph.

Use the Style box to change graph style. Note how the image below uses the heatmap option, which uses brighter shades of yellow to indicate higher-intensity values.

Example graph view

This image shows anther-enriched expression of the AT2G19110 locus. The top graph shows anther data, the middle one shows data from light-grown seedlings, and the bottom graph shows the difference between them, which was calculated using the A-B button in the Graph Adjuster panel. If you follow this link to the TAIR Web site, you will find that experiments using the ATH1 array confirm that this gene is expressed in developing flowers. Based on homology data, it appears to encode a cadmium-transporting ATPase and is localized to the membrane.