Available Nematode Profiles

Experiments

These are a list of the green and red signals from all of the chips. Each experiment compares the green and red signals from one chip.
The first column is the experiment number. The second column is the number of spots on the chip and the chip version number. The third column describes the type of worm used to make the probe.

Groups

"All" shows all the clones on the chip.
"con2" shows just the controls from the chip (about 24 clones).
"all-con2" shows just the Kohara clones.

Click on your chip, then press submit. The program will find all chips that should be identical (same RNAs done on different chips). It then gets the ratio of RED/GREEN for every clone for one chip, and then averages the ratio with the other chip(s). You can see how reproducible the chips signals are by looking at the difference between the chips. We see good reproducibility using the same RNA on different chips.

Expression data

This lists a comparison of all the clones on the chip between your experiment and the control. The genes are sorted by gene expression differences. Genes that are more abundant in your experiment than in the control are listed first. Genes that are missing in your experiment relative to the control are listed last. The list contains genes that are regulated more than 2x.

Rank indicates the rank order of the genes based on gene expression differences. Clicking on the rank number will show you genes that have similar expression profiles, using all of the chips.

Gene indicates the name of the clone. Clicking on the gene name gets you the blast score from KoharaÕs web site.

Log ratio is the ln(signal1/signal2). So a score of 1 means the gene is expressed 2.7x more in the experiment than in the control. A score of -1 means that the gene is expressed 2.7x less in the experiment than in the control. Clicking on log ratio tells you more about the level of expression of this clone.

Function tells you something about the gene. Ultimately, function will tell you the type of protein encoded, and the name of the genetic locus if known. Currently, function tells you the random gene name assigned by Kohara to this particular EST. The expression level is shown in parentheses (See expression level below). Low numbers mean the gene was barely expressed and could fluctuate due to noise.

Click on rank to go to Correlations.
Click on log ratio to go to Expression levels

Expression levels

This shows you how your clone was expressed in all the other chips. For each experiment, the relative signal from your clone (signal from your clone/signal from all clones) is computed. Then each experiment is listed. Experiments at the top are those in which your clone is expressed at a higher level than in your experiment (normalized to all other genes).

Levels tells you the relative expression level for your chip (experiment/control). 1.0 is the mean expression level for all genes. 2.0 means your gene was expressed twice as much as the average gene etc. Baselines tells you the background for that chip, so you know if your expression level is above background.

log ratio tells you how much your gene is regulated in other chips. It shows the natural log of the green/red ratio. A score of 1.0 means the gene is expressed 2.7 times more in the experiment than the control.

Correlations

This tells you what other genes are expressed like your gene, looking at all the different experiments. Genes that are co-regulated with your gene appear near the top, with a correlation score near to 1 (1.00 means identical expression patterns).

There are several caveats in the correlation analysis:
1 - correlations below around 0.7 don't mean much.
2 - there is an expression levels column in the output. The unit is mean gene expression. A score of 1 means this gene is expressed like the average of all genes. Highly expressed genes have a score greater than 1, and lowly expressed genes have a score less than 1. If the gene never gets up to 1.0 don't believe the correlation - there are artifactual correlations in low-level expressed genes arising from the background correction.

To compare one set of targets to another set of targets
goto: wormxcmp4

Suppose you would like to know how one chip experiment (say a Vul mutant) compares to another chip experiment (another Vul mutant). Find the experiment number for the first vul mutant from wormfront2 (experiment 1 is lin-31 in the above example), and set exp#1 equal to that number in the URL. Do the same for the second vul mutant (experiment 2 is let-60(gf) in the above example). Set your reference number to any one of the chip experiments that is within the same class as the ones you want to compare. Then it looks for any gene that moved by 0.75 in at least one of the averages and sorts by how similar the changes were. (You can more than 2 experiments by adding &exp#3=xx etc.)

This is useful to see how similar different RNA batches, different alleles and mutations in different genes are to each other.

To find a specific clone:

Try wormdata1. The text string is used for a case insensitive match on the beginning of the name you see in the output. For example, LIN-1 would find lin-15. The reference experiment picks an experiment to set the baseline as a control.