Short Tutorial Instructions

This short tutorial is for the MAExplorer working prototype. The MAExplorer is an exploratory data analysis facility for microarray cDNA databases from the MGAP project.

  • First, select one of the startup examples from the table of contents on the left or the public or collaborator pages. You should only click once since multiple clicks may cause some browsers to hang. This will begin downloading MAExplorer with a specific set of hybridization probes. If the particular probes you want to analyze are not listed in that example, you will be able to add probes you do want and remove probes you don't want later - regardless of which example was intially used.

    Please be patient after you have invoked MAExplorer while the applet is automatically being downloaded. When it starts, a main window will pop up. It then downloads a clone Id table, the hybridization probes (HP) used in the database and other required data. When it is ready for you to begin interaction, the menu bar will become active. Depending on your Internet connection speed, it may take a few minutes to set up.

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

    HINT: print his page and then read the following instructions from the printout rather than trying to keep this window visible.

    If you are experiencing Web browser problems using the MAExplorer applet, you might check our discussion of possible solutions. NOTES: 1) you may need to resize the windows to view them simultaneously; 2) if you have problems and need to restart the applet on Windows PCs, you should restart your Web browser; 3) MAExplorer as an applet does not currently work well on Macintoshes; 4) we recommend you use Netscape 4.7 or Internet Explorer 5.0 on a Windows PC or Sun computer.

    Instructions for self-guided tutorial of MAExplorer

    The following is a self-guided tutorial (you issue the commands) 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.

    Review of types of clone data available in the database

    step 1: go to GeneClass: All known genes
               the array shows named genes with red "+"s
    step 2: go to GeneClass: ESTs similar to genes
               the array shows ESTs similar to named genes with red "+"s
    step 3: go to GeneClass: ESTs
               the array shows unknown ESTs with red "+"s
    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.C.L." button in pop up window
               Magenta squares will define these genes in the microarray pseudoimage.
               These include the 'onco'genes and the proto'onco-genes

    1. Analysis of the expression profile of a single known gene

    1. ratio between two conditions (e.g. pregnancy and lactation)
    2. profile of a set of conditions
    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 green circle will define the gene as the "current clone" in the microarray
               pseudoimage (info on gene is also provided above the array). F1 and F2 are
               replicate clones (left and right fields) in the array (HP).
    step 5: alternatively, click on an array spot of choice
               to define any clone in the array as the new current clone

    1.1 Two conditions - scatter plots:

    where pregnancy data is on the X axis and lactation on the Y axis
    step 1: click on green 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 clone in the plot as the new current clone
    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
    step 6: go to Plot: Histograms: HP-X/HP-Y
               the histogram shows the ratios
    step 7: move pop up plot so you can see it and the array simultaneously
    step 8: choose (click on) a ratio bin
               clones Filtered by the ratio range of the bin will light up on the array ('+'s)
    step 9: click on different bin in the histogram to select another bin
    step 10: click on word "Freq" on left in histogram to remove the histogram bin filter

    Note of caution: if the signal is close to background the X/Y ratio may be bogus.
    You can filter out low intensity clones by
    step 11: go to Filter: Filter by intensity sliders: Use intensity sliders
    step 12: adjust intensity lower bound (G1) to remove low ratio clones
    step 13: when done, remove the 'Filter by intensity sliders' by toggling it off (see step 11)
    step 11: press "Close" button to remove histogramBR>

    1.2 Multiple conditions - expression profile plots:

    step 1: after the expression profile window pops up, click on a clone in array to see its profile
    step 2: click on a line in the profile plot to see its intensity
    step 3: click on a different clone in the array to see its profile
    step 4: press "Show H.P.s" button to see the list of probes used
    step 5: press "Close" buttons to remove pop up windows

    2. Analysis of the expression profiles of gene classes
    step 1: go to GeneClass: All known genes
               the array only shows named genes (additional gene subclasses are being added)
    step 2: go to Plot: Scatter plots: HP-X vs. HP-Y
               to see the two condition expression of just these clones
    step 3: go to Plots: Expression profiles: Display Filtered clones expression profiles
               to see the multiple condition expression of just these clones. This may take a
               while if there are many clones
    step 4: you can click on a line in any of the plots to see the probe intensity
    step 5: when done, press "Close" button in all pop up plot windows
    step 6: go to Report: Clone reports: Filtered clones: Clones passing Filter
               Clicking on blue entry will bring up I.M.A.G.E, dbEST, UniGene, or GeneBank in pop up Web page
    step 7: press "Close" button in report, and close this pop up Web page
    step 8: go to Report: Table format: Tab-delimited
               to enable creating Excel-compatible reports
    step 9: repeat step 1, but this time to make text-formated report
    step 10: cut the text from this window and paste it into an Excel window
               this is useful for exporting data if you are on a Windows PC
    step 11: go to Filter: all clones
               to restore it to all of the clones from all named clones
    step 12: go to Report: Table format: Spreadsheet
    step 13: press "Close" button in report

    3. Analysis of the expression profile of multiple hand picked genes

    step 1: go to View: Show 'edited clone list'
               this turns on the 'edited clone list' squares overlay
    step 2: hold CONTROL key and click on clones in array to add a clone
    step 2': hold SHIFT key and click on clones in array to delete a clone
               this lets you edit a list of clones. It also works when clicking in a scatter plot
    step 3: go to Filter: Filter by 'edited clone list'
    step 4: go to Plots: Expression profiles: Display Filtered clones expression profiles
               scroll through the plots to see all of the profiles
    step 5: go to Filter: Filter by 'edited clone list'
               this turns off the 'edited clone list' filter
    step 6: press "Close" button in expression profiles window
    step 7: goto Report: Clone report: clones in 'edited clone list'
               reports edited clones
    step 8: press "Close" button in report
    step 9: go to Filter: Filter by 'edited clone list'
               this turns off the 'edited clone list' filter
    step 10: go to View: Show 'edited clone list'
               this turns off the 'edited clone list' squares overlay

    4. Identify clusters of genes with similar expression under various conditions using data mining filters

    step 1: go to GeneClasses: ESTs similar to genes
    step 2: go to Plot: Cluster plots: Display 'N-Primary-Nodes' clustering
               this will pop up a cluster summary and slider control window. Move the summary
               and slider windows so you can see all 3 windows. The size of the
               magenta circles in the array is proportional to # clones/cluster
    step 3: select (click on) a new current clone
               the clones which belong to that cluster are labeled in the array with tiny green numbers are
               defined as the "current cluster". The current clone you click on has a green circle around it

    step 4: goto View: Show 'edited clone list'
               clones in the current cluster were also copied to the edited clone list
    step 5: goto Report: Clone report: clones in 'edited clone list'
               reports clones in the current cluster
    step 6: press "Close" button in report
    step 7: go to View: Show 'edited clone list'
               this turns off the 'edited clone list' squares overlay
    step 8: vary the "# of clusters" slider value from 6 to 10, then 20
               note the number of clusters changes and the clone cluster composition also changes
    step 9: select a new current clone in array and press the "Recompute clusters" button
               this recomputes the clusters using the current clone as the new seed clone
    step 10: press "E.P. plot" button and scroll down the list after they appear
               the primary nodes for each cluster are indicated with red labels in the set of
               profiles, and the other clones are labeled with their cluster number
    step 11: press the "Report" button to get a sorted cluster list
               scroll the spreadsheet to the right to see the cluster statistics
    step 12: press "Close" button in pop up windows
    step 13: go to Plot: Scatter plots: HP-X vs. HP-Y
    step 14: move the plot so you can see both scatter plot and array
    step 15: click on a NPN node in the cluster or on spots in the scatter plot
               note that the green cluster numbers are drawn in the scatter plot

    step 16: go to Edit: Sets of clones : Save 'Edited clone list' as clone sets
               this will pop up a dialog box requesting "Enter new clone set name"
    step 17: type "Clones in current cluster class"            this will save the current cluster in a clone set 6. The clone set will
               be used in the next example
    step 18: press "Close" button in pop up windows

    5. User Clone Set operations
    step 1: go to Edit: Sets of clones : List saved clone sets
               this lists the default clone sets
    step 2: go to Edit: Sets of clones : Set 'use clone set' (for Filter)
               this will request a clone set to use with the Filter in a pop up dialog box.
               Enter '6' which is the set for "Clones in current cluster class" which you saved
               in the previous example.
               then press "Ok" in the dialog box.
    step 3: go to GeneClass: All clones
               this resets the filter to look at all clones
    step 4: go to Filter: Filter by 'useCloneSet' membership
               this restricts the clones to the saved current cluster in the previous example
    step 5: go to Edit: Sets of clones : Union of 2 clone sets
               this will request 3 clone set names in a pop up dialog box.
               Enter '3' (Similar ESTs) for the 1st clone set name,
               Enter '6' (Clones in current cluster class) for the 2nd clone set name,
               Enter "Union of similar ESTs and clones in current cluster" for new clone set name.
               then press "Ok" in the dialog box.
               this computes the union of the two clone sets into a new clone set
    step 6: go to Edit: Sets of clones : Set 'use clone set' (for Filter)
               this will reset the 'Use Clone Set' for the Filter in a pop up dialog box.
               Enter '7' which is the set for "Union of similar ESTs and clones in current cluster"
               just saved.
    step 7: try saving other Filtered clones sets and doing other clone set operations.

    6. Additional tutorials

    If you wish to investigate MAExplorer in more detail, try some of the suggested examples in the     advanced tutorial in the reference manual.

    Revised: $Date: 2001/04/13 17:44:36 $