MAExplorer - Microarray Exploratory Data Analysis

Appendix A. Short tutorial for MAExplorer

This tutorial is for use with MAExplorer, an exploratory data analysis facility for microarray DNA databases. It may be used with any MAExplorer database. As with all tutorials, they are only starting points for getting you started - in this case into understanding the data mining analysis environment. Try out new options on your own, you can't break anything :-).

This tutorial lets you

Analyze expression of individual genes
Analyze expression of gene families and clusters
Compare expression patterns in multiple hybridized samples

NOTE: THIS APPENDIX IS BEING REVISED AND EXPANDED...

A.1 Demonstration data

Note that the downloadable MAExplorer stand-alone application includes a subset of 50 hybridized samples from the MGAP database including a number of startup files for that data (see the the list of startup .mae files included in the download installation).

There is also a pre-computed example of an Ordered Condition List using 4 conditions of replicates of C57B6 (pregnancy day 13, lactation days 1 and 10, and stat5a(-,-) 15 samples. The database also includes 4 additional condition sets of this data and an Ordered Condition List of the 4 conditions (in the State/ directory). This may be used to demo the OCL F-test filter.

If you have access to another MAExplorer database, you can use it instead since the tutorials are fairly generic.

Using the stand-alone application for the tutorial

These same subsets as well as other subsets of the MGAP data are available in the set of .mae startup files distributed with MAExplorer. To access these files,

Start MAExplorer after you have installed it. Eg. in Windows, go to the Windows "Start Menu" and click on MAExplorer. If it is not in your Start Menu, you can go to where you installed it (typically C:\Program Files\MAExplorer) and click on MAExplorer.exe.
Then after it starts, go to the "Files" menu and select "Open disk DB" and select the startup file you want. Alternatively, you can go directly to the list of startup files in C:\Program Files\MAExplorer\MAE) and double-click on one of the startup files.

A.2 General instructions:

Throughout this tutorial we refer to condition X and condition Y. These are different hybridized samples in the particular database you have loaded. For example, in the MGAP database X might be lactation and Y might be pregnancy. X and Y 'sets' are multiple samples of these two conditions.

First, select one of the start up databases.

As a stand-alone application, select the startup file entry (files ending with a ".mae" file extension) from a directory of startup files on your local computer. Generally these are in a subdirectory called MAE in a project directory (see Appendix C. Use of MAExplorer with other microarrays).

If the particular samples you want to analyze are not listed in that example, after it starts you will be able to add samples you do want and remove samples you don't want - regardless of which example was intially used if the database "Samples" database contains additional hybridized samples.

When it starts, a main window will pop up. It then downloads a gene database tables and the particular hybridized samples you specified. When it is ready for you to begin interaction, the menu bar will become active and it will display a green Ready - click on a gene to query database message. Depending on your Internet connection speed, it may take a few minutes to set up. If you are running MAExplorer as a stand-alone application and it is getting data from your local disk, startup will be much faster.

Second, go to the A.3 instructions for self-guided tutorial below for instructions on what to do next.

HINT: print this tutorial page and then read the following instructions from the printout rather than trying to keep this window visible. You might also print the parts of the MAExplorer Reference Manual for the same reason.

HINT: You might want to keep a record of the commands you have used or the messages and measurements you have made. To do this you need to enable message and command history logging. Go to the View pull-down menu and then select the type of logging you want using the Show log of messages or the Show log of command history commands.

NOTES:. On computers with low resolution (i.e. less than 1024 X 780) you may need to resize the windows and move them to different parts of the screen to view them simultaneously.

A.3 Self-guided tutorial of MAExplorer - notation and examples

The following is a self-guided tutorial (you issue the commands) that illustrates some of the data analysis capabilities. In the following examples, the notation "go to A:B:C" means go pull-down menu A, then submenu B and, then make selection C. "Selecting a gene" from the microarray image or scatter plot means clicking on a spot in the pseudoarray image or a point in the any of the plots.

A.3.1 Review of types of gene data available in the database

A.3.1.1 Analysis of the expression of a single known gene

ratio between two conditions X and Y (HP-X, HP-Y)

expression profile of a set of conditions (HP-E) (see Example A.3.1.7)

step 1: click on the blue "Enter gene name" button to pop up a name entry window
step 2: start typing gene name into blue text entry window
step 3: once gene names appear, click on gene of choice
step 4: press "Done" button in pop up window
           A yellow circle will define the gene as the "current gene" in the microarray
           pseudoarray image (info on gene is also provided in the status area above the array).
           If there are replicate grids (left and right fields of repeated genes are denoted
           by F1 and F2) in the array (HP). The mean(HP-X,HP-Y) values and the (HP-X/HP-Y)
           values for the specified gene are reported are reported.
step 5: alternatively, click on an array spot of choice to define any gene
           in the array as the new current gene

A.3.1.2 Find a subset of genes with a common substring (e.g. ONCO)

step 1: click on the blue "Enter gene name" button to pop up a name entry window
step 2: start typing "*ONCO*" (without the quotes) into blue text entry window
step 3: once gene names appear, press "Set E.G.L." button in pop up window
Magenta squares will indicate these genes in the pseudoarray image.
These include the 'onco'genes and the proto-'onco'genes

A.3.1.3 Two conditions - scatter plots:

Create a scatter plot of two hybridized samples where condition X data is on the X axis and condition Y data on the Y axis.

step 1: go to Analysis: Plot: Scatter plots: HP-X vs. HP-Y.
then click on yellow circle in scatter plot to get HP-X/HP-Y ratio for the gene
step 2: click on any point in the scatter plot
this also alternatively defines any gene in the plot as the new current gene
step 3: zoom in on a region of the plot using the vertical or horizontal scroll bars
step 4: click on another point in the scatter plot to get the HP-X/HP-Y ratio another gene
step 5: press "Close" button to remove pop up window

A.3.1.4 Scatter plot of Cy3 vs Cy5 or replicate spots (F1 vs F2) of one sample

Create a scatter plot of Cy3 vs Cy5 channels or replicate spot F1, F2 data if your database is contains (Cy3,Cy5) ratio data or it contains replicate spot fields (F1,F2).

step 1: go to Analysis: Plot: Scatter plots: Cy3 vs. Cy5
           or go to Analysis: Plot: Scatter plots: F1 vs. F2
           Then, click on green circle in scatter plot to get Cy3/CY5 ratio for the gene
           or F1/F2 ratio for replicate spots for that gene
step 2: click on any point in the scatter plot
           this also alternatively defines any gene in the plot as the new current gene
step 3: zoom in on a region of the plot using the vertical or horizontal scroll bars
step 4: click on another point in the scatter plot to get the HP-X/HP-Y ratio another gene

If you are working with Cy3/Cy5 dye-swap data, you may swap the Cy3/Cy5 channel data to Cy5/Cy3 for any selected subset of samples. This may make it easier to use the data in various ways when data mining. If you do not have this type of data, go to step 7.

step 5': go to Samples: Edit (Cy5/Cy3) else use (Cy3/Cy5) menu
step 6': select the samples you wish to swap and press "Done". This
enables you to see the swapped results in the scatter plot
step 7: press "Close" button to remove pop up window