Slide 1. GEB Home Page
User can enter an search word in the home page. In the example, we try to discover plant disease related gene expression profiles so that enter famous Arabidopsis disease-related gene name 'pr1' as search key.
Slide 2. Search Result Page
Click submit button after entering key word 'pr1' and get the search result page. One item is in the result list: PR-1 gene with Affymetrix ID of 266385_at and locus ID of At2g14610. Click the link on Affymetrix ID to visit the Gene View of PR-1 gene.
Slide 3. Gene View of PR-1 gene
MA plot is used for presenting Gene View. Each point on the MA plot is a T/C. A red rectangle square is at top-left corner. You can drag-and-drop the square onto data pointer to highlight the data points and get the detailed information. Meanwhile, you can also enter a word as search key to search the data points.
Slide 4: Search Data Points
As we knwo, PR-1 gene is disease-related genes. Therefore, we want to know how infection related T/Cs affect the gene expression. Enter 'infection' as key word and click 'Search T/C' button. The search result items are listed. A lot of virus/bacteria/fungi infection experimental T/Cs are in the result list.
Slide 5: Select T/Cs from search result list
Select 23 data items of Pst DC3000 infection T/Cs. The selected items are marked in MA plots and also listetd in the bottom box. We can observe that half Pst DC3000 infection T/Cs up-regulate PR-1 genes and half of them do not change the gene expression.
Slide 6: Change color of data point markers according to infection time.
We noticed the long-time infetion T/Cs causes the increase of PR-1 gene while short-term infections do not change the gene expression. We change the data markers of short-term infection (6 hr or less) to black and keep 7 hr or more infections as red. We can see that most long-term infections induce the expression of PR-1 while short-term infections do not have obvious effects.
Slide 7: Hightlight data points
Drag-and-drop the red square in topleft corner onto the data points of up-regulation T/Cs. You can adjust the size of red square by drag its right-bottom corner. All data points covered by the red square are listed in the left box. We notice that many diease-related T/Cs in the list. The first item is 'BTH Effect for 24 hr in wrky18 mutant'. Click on the link and get a T/C View.
Slide 8: T/C View of 'BTH Effect for 24 hr in wrky18 mutant'
T/C View is also shown by MA plot. Each data point on the T/C View is a gene. Just like Gene View, user can explore the data points by searching and highlighting. Close the T/C View and go back to the Gene View of PR-1 gene.
Slide 9: Select disease related T/Cs
A group of up-regulation T/Cs are highlighted in slide 7. There three kinds of disease related T/Cs: (1)virus/bacteria/fungi infection (Pst DC3000, Erysiphe orontii, Phytophthora) (2)Disease-resistant mutants (cpr5, cpr5scv1, snil). (3)SAR (Systemic Acquired Resistance) that is caused by BTH (Benzothiadiazole S-methylester). Click 'select' links to select 15 disease-related T/Cs. Then, click [Slides] link to view all slected T/Cs in a slides show.
Slide 10: Slides show of 15 disease related T/Cs
User can use red square to hight data or search data by entering word. User can move to next slide by clicking right arrow or move to previous slide by clicking left arrow.
Slide 11: Select data points in Slides View
Move to the 3rd slide 'Pst DC3000 infection (12 hr) in WT (3/15)'. Drag-and-drop the red square to cover the up-regulatd genes and the highlighed genes are listed in left box. Select the genes with 20-fold increase and the p-value of 0.01 or less. 86 genes are selected and marked. Click right arrow to move to next slide. The selected data points are re-distributed in next slide.
Slide 12: wrky17 mutant with Pst DC3000 infection
wrky17 is very similar to wild type when they are infected by Pst DC3000 for 12 hr. This shows that the plants with differnt genetic backgrounds have similar gene expression profiles when they are infected by Pst DC3000.
Slide 14: Erysiphe orontii infection
About 90% Pst DC3000 induced genes are also induced by Erysiphe orontii infection.
Slide 15: Phytophthora infection
About 70% Pst DC3000 induced genes are also induced by Phytophthora infection.
Slide 16: cpr5 mutant
About 90% Pst DC3000 induced genes are also induced in cpr5 mutant. It is very interesting. As we know, cpr5 is disease-resistant mutant. This can explain why cpr5 is disease-resistant.
Slide 17: cpr5scv1 mutant
About 95% Pst DC3000 induced genes are also induced cpr5scv1 mutant. Very interesting!
Slide 17: sni1 mutant
About 60% Pst DC3000 induced genes are also induced sni1 mutant.
Slide 18: SAR (Systemic Acquired Resistance) is caused by BTH(Benzothiadiazole S-methylester) treatment
About 70% Pst DC3000 induced genes are also induced BTH treatment. It can explain why BTH causes SAR!
