BirdsEyeView Manual

 

1. Run BEV:

BEV uses Java Web Start technology so that users do not need to install the program or download it to run BEV. If users’ operating system has already installed latest Java platform, users can click the link on our website to run BEV directly. Relative Java running information dialogs will be shown after the click. After that, BEV will show its splash window and download some required data from database at the same time as Figure 1 shows.
Start hint
Figure 1 Starting hint picture

2. Open file:

After downloading data, the main interface of BEV will be shown and it is ready to accept imported data file and show them on the map. To open a file, click the open file icon (as in the Figure 2) on the menu bar of the main window.
Open file icon
Figure 2 Open file icon
A file open dialog will be opened after the click. BEV supports two file types: separated data files and integrated data files. Separated files use 3 different files to store information: probes file containing the list of probes (biomolecules) in the experiments, chips file containing the list of chips (experiments), and the pure data file (numbers). The integrated file contains three kinds of information together. It should be in a format of comma separated file. Users can choose any one of file type and then input the file name as in Figure 3.

3. Load data:

After users give the data file, BEV will load information about each entity (Gene) in the data file. Depends on the number of entities in the file, BEV shows the loading status as a progress window like Figure 4.

data loading status window
Figure 3 data loading status window

File open dialog
Figure 4 File open dialog

Cell view after file loaded
Figure 5 Cell view after file loaded

4. Mapping data and information display:

 

4.1 Results display:

Once data loading finished, the entity information will be shown in the mapping views of main window. BEV provides 4 mapping views: cellular view (Figure 5), pathway view (Figure 6), Gene Ontology function view (Figure 7), and Gene Ontology process view (Figure 7). Users can switch among them by using the leftmost combo box of button panel (Figure 8). BEV uses the information stored in MetNetDB and data in the experiment data file to give users an overview of the experiment data on different maps (cell, pathway and Gene Ontology). It gives users a unique view of experiment result by mapping the experimental entities (genes or others biomolecules) on different views based on those entities profile information in MetNetDB. The entities are represented by a rectangle or a circle in the view. When a user moves his mouse over the entity unit (rectangle or circle) in the view, a hint information window about the current unit will be shown besides the unit as in Figure 9. The name and the relative value (expression level, etc.) of the unit will be shown in the hint window if the unit is a circle (i.e., it only represents one gene or entity) and the number of genes and the average value will be shown if the unit represents multiple genes or entities. In addition, if the mouse is over a compartment in the cell view, or a pathway box in the pathway view, or a Gene Ontology rectangle in Gene Ontology function view or Gene Ontology process view, the name of the relative container and the number of genes or entities in the container will be shown in a hint window besides the rectangle as in Figure 10.
Different views switcher
Figure 6 Different views switcher

Pathway view
Figure 7 Pathway view

Gene Ontology view
Figure 8 Gene Ontology view
Entity unit hint information window
Figure 9 Entity unit hint information window

Compartment hint information window
Figure 10 Compartment hint information window

To see more detail about content of an entities representing unit, a user can click the rectangle or circle by left key of mouse and the information will be shown in the bottom part or text panel of the main window. The panel displays list of detail information of entities. Figure 11 shows the display result of clicking a rectangle representing 3 genes in text panel. Meanwhile, once clicked, the unit on the view will be highlighted by blue color as in Figure 12 and its information will be kept in text panel. Each time a mouse moved over the entity, the text panel will scroll to the place of information list of representing unit and the rows in the list will be high lighted by blue color as in Figure 11.
Therefore, all units on mapping view highlighted by blue color get their information shown in text panel. Users can click again on the unit to cancel it and then the unit will resume to original color and the information rows in text panel will be removed. To remove all information rows in text panel (i.e. to unselect or unhighlight units on mapping view), users can right click mouse on a highlighted unit and a menu will be pop up. The first choice is to clear all highlights. The second choice will open a web browser to browse full information list store on MetNetDB about the entity or the entities group as shown in Figure 13.

 

Text panel displaying detail information
Figure 11 Text panel displaying detail information

Entity selected
Figure 12 Entity selected

Right key popup window
Figure 13 Right key popup window

 

4.2 Adjusting parameters of display:

The color of each unit on the mapping view is automatically evenly arranged by the range of inputted data. The deeper color, the higher value of the data or the average data that one unit represents. The user can also adjust the color range value. In the legend panel shown in Figure 14 (users can show or hide it by click relative button on the button panel), the color setting for data value is shown with other parameters setting. Users can adjust “the number of genes each unit represents” when some units need to represent multiple genes for limit size of containers. The number has a minimum limit to make all genes displayed. Users can make it bigger so that there will be fewer units on mapping view. As introduced above, the text panel displays detail information for each unit. If there are many entities represented by one unit, displaying all of them on text panel may not be troublesome to locate a special one for limit space of text panel. BEV opens a new frame to display detail information of one unit if the unit represents more then 10 units by default. Users can adjust this value in the legend panel. In addition, users can also set a cut value to let BEV show the entities with special value (> or < some number) only on the mapping view. Figure 15 shows the result when users set the number of genes represented by each unit to 11 and changed some color strategy with the same input data of Figure 5.
Legend and parameter adjust panel
Figure 14 Legend and parameter adjust panel


Cell view after some parameters changed
Figure 15 Cell view after some parameters changed

 

4.3 Experiment comparison
Besides showing content of single experiment, BEV can also compare results of two different experiments.  To compare, make the single option box on button panel selected, then you can choose two different experiments to compare. There are three types of comparison: difference, doing subtraction between two experiment results; fold, dividing the first experiment result by the second one; difference fold, dividing the difference between two experiments by the second experiment result. Users can choose one of them from the drop-down list in the combo box following the option box as shown in Figure 16. Figure 17 shows the result of fold comparison of between experiment “ws 1.0m” and “ws 1.30m” in the same data file of examples above.

4.4 Display multiple views

BEV can also show two views together. Users can choose the “Show two views together” in the switch view box as Figure 6 and then a two views choice dialog will be opened as in Figure 18. Figure 19 shows the result if choosing cell view and pathway view to be shown together.
To compare two experiments
Figure 16 To compare two experiments

Cell view for fold comparison of two experiments
Figure 17 Cell view for fold comparison of two experiments

Two views display choice
Figure 18 Two views display choice


Showing two views together
Figure 19 Showing two views together