Introduction to Expressionanalyzer

Introduction to ExpressionAnalyzer

Open the Software

Double click on ExpressionAnalyzer

Creating a new Study

After pushing the button for creating a new study a file open dialog will popup from which the user can choose the Affymetrix® Expression Console™ output file that he wants to use with the tool and a new study name can be typed in. A dialog will inform the user if this study exists. After hitting Enter a new database will be created and the user will reach the rename layout.

Rename the column names

In this window the user is able to rename the column names which came from the Affymetrix® Expression Console™ output file. So the user can use his own titles for description fields and intensity fields. Special characters like spaces can’t be typed in. All column names have to be unique otherwise there will popup an error dialog which will inform the user to rename it. A name for a column is limited to ten characters.

After renaming the user hits enter. The new column names will be applied and data will be imported in the database. This can take several minutes. After creating the database the user will reach the search window which will be described later.

Open an existing Study

By clicking the “open an existing Study” button a popup window will come up which contains a list with studies the user can open and the next button. After choosing a study and clicking next the search layout will be shown.

Delete an existing Study

By clicking the “delete an existing study” button a popup window will come up which contains a list with studies the user can delete and the delete button. After choosing a study and clicking delete the chosen study will be deleted.

Configure Database

To connect with MySQL the tool needs the MySQL username, the host and password.

So if the user clicks “Configure Database” a popup window will come up where the user has two options; default and advanced.

If the user chooses the default option he needs to have a MySQL user named root with password 0000 and host "jdbc:mysql://localhost:3306". How this MySQL account is created is described at the webpage under “How to install MySQL”.

If the user clicks on the advanced option, a popup window is shown where the user can type in a user name, password and host. By clicking on the save button this modification will be stored.

Connection Errors

If the user tries to create, delete or open a study without the correct database account configuration an error dialog will be shown and the configure database dialog will popup. The user has to reconfigure the connection details as described before.

Do a search

The search Layout allows the user to search for fold change, intensities and description. For convenience the last search criteria are always saved but the user can clear all field with the “Clear” button. The button “Sets” brings the user to the list of sets that he has already made. The button “Display Options” will open a window where the user can choose which fields he wants to see in the results table. To perform a search the user can either click enter or the “Find” button either brings him to the results table.

How searching works

If the user chooses „WL01 foldchange 2 greater WL02“, this displays all the genes which have WL01/WL02 >= 2 , otherwise if the user choose „WL01 foldchange 2 smaller WL02“ this displays genes for which WL02/WL01 >= 2. The user can also type minimum intensity values, restricting the genes displayed to those which have achieved a critical level of expression. If the user searches for description fields he can just enter a part of the word that he is searching for. All matches which achieve all other given criteria’s will be displayed.

Display Options

Display options opens a window which contains checkboxes for all possible comparisons between the arrays. So if we have 16 arrays in the study it will contain 256 checkboxes. 240 possible comparisons between different arrays with 16 “self” comparison boxes being used to toggle display of intensity data. So if the user checks the box WL01 vs. WL01 only the intensity values from WL01 array will be displayed. On the other hand if the user chooses WL01 (vertical) and WL02 (horizontal) the result of the WL02/WL01 comparison will be shown. With the button “Save” the user can save his comparisons and whenever he makes a new find these columns will be shown in the results table. The button “Signals” will check all intensity values from all arrays lie all on the diagonal line. “CheckAll” button will check all fields, but in the results table only 30 columns can be displayed. UncheckAll clears all chosen checkboxes. The “Description” button opens a window from which the user can chose the description fields which he wants to display.

Description

Description opens a window where the user can chose the description fields he wants to display. For multiply selection, the Ctrl key can be hold down. By clicking the “Save” button the chosen description fields will displayed in the results table.

Result Table

All results are displayed in a table. If the user double clicks in a field of the table a window will popup with a scrollbar to see all the text in the field. The user can widen and condense columns, by dragging their margins, and by clicking on the header the table will be sorted. To alter the table contents the user can click on “Display Options” and use this window as described previously. The header of this layout contains a field “count” which shows the user how many genes are in the current table. The button “Find” brings the user to the search Layout as described before. By clicking the “Save” button these genes are saved as a Set and the user is taken to the Sets Layout as described below. The “Sets” button brings the user to the table where he can look at his sets (described below). By clicking the “Venn” button the user will come back to the last Venn diagram, if there is one. By clicking the “Print” button the current table contents can be printed and the “TXT” button allows the user to print the table contents in a text file.

Sets Table

The Sets table displays all the Sets that the user has already saved. Every row contains six fields. SetsID (unique Number for the Set), Name (name of this Set), Count (Amount of genes in the set), a “View” button to display the genes in a set, a Checkbox to select a Set for drawing an Venn diagram or exporting the set to txt, and a “Delete” button to delete the set. By clicking in the name field the user is able to alter the name whenever he wants. In the header there are four buttons. The “Find” button brings the user back to the search layout. The “Venn” button draws a Venn diagram when two or three sets are selected. When less sets are selected the latest Venn diagram will be shown and when more are selected the first three will be used for drawing it. The “Export” button allows the user to export sets and use them in other studies. By clicking the “Import” Button the user is able to import sets from a file created by this tool.

Venn Diagram

The Venn diagram can be drawn for two or three Sets. With the button Sets the user can go back to the sets layout. The Venn diagram itself has many buttons showing the number of genes in each sub-set. The button “Set1” only represents the genes which are in Set1 and not in Set2 or Set3. By clicking on it all genes which are in Set1 and not in Set2 or Set3 will be displayed.