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Let's learn how to use GEB by an example. We try to compare the gene expression profiles among virus/bacteria/fungi infection, disease-resistant mutants or the conditions of Systemic Acquired Resistance (SAR). In order to have the best visualization effects, please set the resolution of your computer monitor to 1280X800 or 1280X960. Firefox 3 is the best browser for visualizing the application though IE 7.0 and Safari 3.2.1 are also tested. Screenshot images are listed on the right column. Please move your mouse pointer onto the images to obtain the description of each screenshot. You can also finish the training by viewing slide show or Shockwave flash video show or video show in Youtube (watch in high quality)
Visit GEB home page and enter key word "pr1" (pr1 is an Arabidopsis disease-related gene) and click submit. An item of Arabidopsis pr1 gene (At2g14610) is listed in the search result list. Click the link of on Affymetrix feature identifier 266385_at to see the Gene View of PR-1 gene in GEB.
Gene View
GEB Gene View displays all T/Cs (Treatment over Control) that regulate the gene in MA plot. The MA plot is on the left and two list boxes are on the right. A red square is located on the up-right corner of the MA plot. User can drag-and-drop the red square onto data points to find the detailed information of the data points. Each data point on the MA plot Gene View is a T/C (Treatment over Control). The data points are painted with blue, green and yellow. Blue data points have the p-values (t-test treatment vs control) of less than 0.01. Green data points have the p-values of 0.01 - 0.05. Yellow data points have the p-values of 0.05 or higher. The Y-axis is log2 ratio of treatment vs control. The treatments have higher expression than controls (up-regulated) in the data points on upper positions. On the other hand, the treatments have lower expression than controls (down-regulated) in lower poisitions. A horizontal zone on the middle position represents 1.5-fold (log2 ratio 0.58) up-regulation at its upper edge and 1.5-fold (log2 ratio -0.58) down-regulation at its down edge. X-axis is the average intensity of treatment and control. The right positions on MA plot mean higher expression signal in treatment and control and the left positions mean lower expression signal. A vertical zone represents background signal levels. In this Gene View of pr1, we can observed that many blue data points are located on up or bottom positions. On the other hand, most yellow points are located on the middle positions.
Search data points
User can locate the T/Cs on the Gene View by searching them using key words. As we know, PR-1 gene is disease related gene. Try to use key word 'infection' as search key. In next screen shot, type key word 'infection' into text box and click 'Search T/C' button. Many T/Cs that contain 'infection' appears in the display box. Select 23 items of 'Pst DC3000 infection' and the 23 data points are marked with small red rectangles on MA plot and the data items are listed in select box. About half selected items are up-regulated and half items are in the middle zone (no obvious changes between treatment and control). I try to separate the 23 selected data points into two groups: infection for less than 6 hr and infection for more than 7 hr. Click the color square in select box and a color picker pops up. Select black color on the color picker to change the color of data points that are less than 6-hr infection. We can see that most long infection items (red data points) are up-regulation. On the other hand, short infection (black data points) mostly does not change the expression of pr1.
Highlight data points
Users can drag-and-drop the red square onto data points and then the detailed information of the data points are displayed in the up-right list box. Move the red square onto up-regulation T/C data points and a list of T/Cs are listed in the display box (right-top box). The first item is 'BTH Effect for 24 hr in wrky18 mutant'. Click the link on this item to visit T/C View of this item. Close the T/C View window and go back to PR-1 Gene View. Only disease-related T/Cs are selected in this example. There three kinds of disease related T/Cs: (1)virus/bacteria/fungi infection (Pst DC3000, Erysiphe orontii, Phytophthora) (2)Disease-resistant mutants (cpr5, cpr5scv1, sni1). (3)SAR (Systemic Acquired Resistance) that is caused by BTH (Benzothiadiazole S-methylester) treatment. Click 'select' links of all these disease-related T/Cs. The selected data items are listed in bottom-right list box and the data point in MA plot is marked with a small red rectangle. Click [Slids] link to see the Slide View of selected T/Cs.
Slides View
Slide View shows the gene expression profiles in a group of T/Cs or a group of genes. In this example we selected 15 disease-related T/Cs and then click [Slide] link to view the Slide View of these 15 selected T/Cs. T/C Slide View is similar to T/C view. A right arrow at right of MA plot image is used for viewing next slide. A left arrow at the left of MA plot image is for viewing previous slide. Click right arrow to the 3rd slide "Pst DC3000 infection (12 hr) in WT (3/15)". Use red square to highlight up-regulated genes in this T/C View slide. Select 86 genes that are 20-fold increased by Pst DC3000 infection and p-value less than 0.05. The data points of the selected 86 genes are marked with small red rectangle. Click right arrow to view next slide and see the selected data points are re-distributed in the next slide. Following Figure shows the expression changes of the 86 Pst DC3000-induced genes. We can observe most the genes are also increased in other infection conditions and in disease-resistant mutants and in SAR conditions.
Conclusions
Many genes are increased after the Arabidopsis plants are infected by Pst DC3000. 86 Pst DC3000 up-regulated genes are selected. Most of these 86 genes (60% - 95%) are also increased in other infection conditions, disease resistant mutants and the conditions of SAR. Therefore, we can conclude that there are common gene expression profiles among disease infections, disease resistant mutant and SAR conditions. It would be interesting to further explore the similarities and differences among different infections, mutants and SAR conditions.