PUMAdb : How to use Spot History

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How to use Spot History

This is a compilation of the expression level of the clone you specified in all microarray experiments to which you have access. The value plotted is the log-transformed, normalized ratio of the intensities (i.e., expression levels) in the two channels (probes) in each experiment. No averaging is done; each instance "spot") of the clone is treated separately. Note that there may be fewer spots than arrays to which you have access, even if the clone appears on those arrays, if the spot was flagged as bad on some of them.

Coloring is by the normalized intensity measurements of each spot. Spots for which both intensity measurements were above the specified cutoff are represented by dark green bars. Spots for which one or both measurements were below the cutoff are represented by yellow bars, which "float" above the green bars. This is intended to make it easy to see the distribution of spots with good intensity. The one exception arises if you entered the program by selecting an individual spot to examine; that spot is always represented in dark blue, below any other spots that may share a bar with it. You can change the cutoff value (decimal numbers only, please) using the dialogue box beneath the histogram.

To see which spots fall within a given range of values, click on any bar of interest on the graph. You may click on any number of interesting bars; they do not need to be contiguous. Selected bars will appear with a green mark above the top of the bar. As you select each bar, a list of the experiments with values in that range will appear to the right of the histogram. Clicking a second time on a bar will unselect it, removing the mark and adjusting the list.

If a selected experiment is on an array with multiple instances of the clone, all instances will be shown, whether or not they fall in the selected range. This allows you to determine at a glance whether the behavior of the various spots was consistent. The spot number is displayed for each instance, allowing precise comparisons across experiments, and the normalized red/green intensity ratio. Coloration follows the same rules as for the graph, described above.

There are several ways to use the list of experiments. You can (un)select desired experiments using the checkbox next to each listing. Clicking on the "Display Data" button will give you a list of the selected experiments with more complete information, and further options for viewing data. Clicking on the "Data Retrieval and Analysis" button will take you to the clustering utilities with the selected list of experiments. Clicking on the "Zoom" link next to a spot will give you a close-up view of the spot with a plethora of descriptive and statistical information about it. Finally, clicking on the "Whole" link next to a spot will show you an image of the microarray on which it appears, with the spot in question marked (you may have to do some hunting to find it on the array).

You can get a tab-delimited, spreadsheet-friendly file of all the data contained in the histogram by clicking on the "Download data" button. The page will be redisplayed with a link to the file, "Click here to download data," at the top and bottom. The name of the file will contain the SUID; if you want a better annotation, save the file under a different name.

Note that you must be logged into the database to use any of the functions available from the list of experiments. If you are not already logged in, an attempt to use them will take you to a login page. If you do not have an database account, you can click on the "Public Search" button on the login screen. You can then use your browser's Back button to return to the Spot History program (you may have to click the Back button twice in quick succession to escape the automatic redirect to the login screen), and continue.