ProtPlot Menus

Menu Descriptions for ProtPlot

• Clicking on a protein spot in the scatterplot
• Adjusting the Mw and pI sliders for the scatterplot
• Selecting commands from the pull-down menu bar at the top of the window
• Adjusting threshold sliders on the right
• Selecting samples in the pull-down menu in the lower left menu bar
• Toggling frequently used checkbox options in the lower menu bar

These controls are shown in the following figure:

Interrogating the database by clicking on a spot in the scatterplot

• Single sample: it will report expression data on only that sample.
• Mean samples (EP set): mean expression, std-dev expression, Coefficient of Variation (CV) of expression, number of samples.
• (X sample)/(Y sample) ratio of 2 samples: for both the X and Y sets it reports the expression and the ratio (X sample)/(Y sample).
• (Mean X-set)/(Mean Y-set) ratio of samples: for both the X and Y sets it reports the mean expression, std-dev expression, CV of expression, number of samples. In addition, it reports the ratio computed as (Mean X-set)/(Mean Y-set).

Mw and pI upper and lower limits sliders

The upper and lower limits of Mw and pI may be controlled directly thorugh sliders on the left and right respectively as shown in the following figure.

The continuous parameter threshold slider controls

Parameters may be defined interactively using direct manipulation sliders on the right side of the main window. These right slider controls include:

• Expression upper limit - this adjusts the upper limit of the expression data filter (while in expression mode)
• Expression lower limit - this adjusts the lower limit of the expression data filter (while in expression mode)
• Ratio upper limit - this adjusts the upper limit of the ratio (X/Y) data filter (while in ratio mode)
• Ratio lower limit - this adjusts the upper lower of the ratio (X/Y) data filter (while in ratio mode)
• Cluster distance threshold - this adjusts the D cluster distance parameter if clustering is active in "Mean EP display mode"
• P-value threshold - this adjusts the p-value parameter if the t-Test or other similar filtering is enabled
• # samplesthreshold - this adjusts the N samples parameter if the minimum or maximum number of samples filtering is enabled
• # proteins/sample threshold - this adjusts the S proteins/sample parameter

Samples menu and checkboxes in the lower command bar

These lower controls include:

• A pull-down sample selector to let you redefine the current sample, X sample, Y sample, X-set of samples, Y-set of samples, and EP (expression profile) list of samples.
• Use XY-sets - this toggles between the ratio (Mean X-set / Mean Y-set) of samples mode and the previous display mode
• Expression - this toggles the displaying the spots in the pseudo 2D-gel as colored expression values or simply location
• Low Mw - this toggles displaying the Mw scale as a log(Mw)
• Mouse-over - this toggles the mouse-over option. Holding the mouse over a spot will display its annotations
• Status popup - this toggles the popup status window on and off

Pull-down menu commands in the upper menu bar

The top pull-down menu selections include commands which invoke an action, checkbox options [CB] which are independent of one another, and radio button options [RB] which may only have one member active at a time. Menu entries followed by the symbol, indicate that the menu entry has a submenu. Selections prefaced with a '' and indicate '' indicate that the command is a checkbox that is enabled and disabled respectively. Checkbox menu items have a "[CB]" at the end of the command. Selections prefaced with a '' and indicate '' indicate that the command is a multiple choice "radio button" that is enabled and disabled respectively, and that only one member of the group is allowed to be on at a time. Radio button menu items have a "[RB]" at the end of the command.

There are a number of pull-down menus in ProtPlot including:

1. File - select samples, save the state and quit
2. View - select viewing options
3. Genomic-DBs - enable access to popup Web genomic databases
4. Filter - select protein data filter options
5. Plot - select primary plot mode and plotting options
6. Cluster - select cluster distance metrics and perform clustering
7. Report - generate popup reports
8. Help - the help menu - local and server based

• Select samples
  • Select Current PRP sample - select sample for expression mode
  • Select X PRP sample - select X sample for use in X/Y ratio mode. If use sample sets mode is on, then define the X set.
  • Select Y PRP sample - select Y sample for use in X/Y ratio mode. If use sample sets mode is on, then define the Y set.
  • Select Expression List of samples - the subset of samples is used in Expression Profile Plots and in clustering
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  • List sample assignments - for current, X, Y, and X set, Y set and EP list
  • Assign X set name - to assign a new condition name to the X samples set
  • Assign Y set name - to assign a new condition name to the Y samples set
• Find proteins
  • Find protein by SwissProt Acc - if the SP-ACC is in the database
  • Find protein by SwissProt ID - if the SP-ID is in the database
• State
  • Reset State - set the state to the defaults
  • Protein Sets
    • Open Cluster protein set file from .set file - change the saved Cluster set to one you specify contained in a Set/*.set file.
    • Open Filter protein set file from .set file - change the saved Filter set to one you specify contained in a Set/*.set file
    • Save Cluster protein set file to .set file - save the saved Cluster protein set to one you specify in a Set/*.set file.
    • Save Filter protein set file to .set file - save the saved Filter protein set to one you specify in a Set/*.set file
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    • Set Filter set to Intersection of two .set files - set the saved Filter protein set to the intersection of previously saved protein set files.
    • Set Filter set to Union of two .set files - set the saved Filter protein set to the Union of previously saved protein set files.
    • Set Filter set to Difference of two .set files - set the saved Filter protein set to the difference of previously saved protein set files (proteins in first file but not in the second).
  • Open State file - change the state by reading the previously saved startup file and the saved cluster and filter sets.
  • Save State - save the state and saved protein sets as State/*.prpstate and Set/*.set files and continue the program
  • Save As State - same as "Save State", but prompt for a different state file name to use
  • Save State and Close - save the state and exit the program
• Update
  • Update ProtPlot program from TMAP ProtPlot server - get latest version
  • Update PRP data files from TMAP ProtPlot server - get latest version
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  • Use new PRP data file with this working database - lets you use other in the current running database. The samples may derived from CGAP or from other sources (see .prp data file format)
  • Add new .prp file to your local PRP directory - lets you add other samples to your local PRP database. The sample may be derived from CGAP or from other sources (see .prp data file format).
• Close - exit the program, do not save state

• Filter proteins > 200K Daltons [CB] - enable to use all proteins, otherwise just use those below 200K Daltons
• Filter data by protein families [CB] [FUTURE]
• Filter data by tissue types [CB] - to filter by a subset of tissues
• Filter data by expression (or ratio) range [CB]
• Filter by (X/Y) outside [minRatio:MaxRatio] sliders [CB] - only for ratio mode else filter by inside ratio range
• Filter by X & Y sets t-test results [CB] - do t-test if using X and Y sets
• Filter by X & Y sets Kolmogorov-Smirnov test results [CB] - do test if using X and Y sets
• Filter by X & Y sets missing and > N samples [CB] - present in X or Y set with > N samples using the slider 'N' and is completely missing in the other set
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• Filter by requiring at least N samples [RB] - using the slider 'N'
• Filter by requiring ayt most N samples [RB] - using the slider 'N'
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• Filter by Saved Clustered proteins [CB] - the clustered proteins set may be created when doing clustering by pressing the "Save Cluster Results" when clustering
• Filter by Saved Filtered proteins [CB] - the filter proteins set may be created by pressing the "Save Filtered Results"

• Show current sample expression data [RB]
• Show mean EP-set samples expression data [RB]
• Show X-sample/Y-sample ratio (Red=X + Green=Y) data [RB]
• Show X-sample/Y-sample ratio range color map [RB]
• Show X-Set-samples/Y-Set-samples ratio range color map [RB]
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• Display (X vs Y) else (Mw vs pI) scatterplot - if ratio mode [CB] - if in X/Y or X-set/Y-set ratio display mode, then display the X-Y scatterplot instead of the Mw vs. pI scatterplot.
• Save scatterplot as GIF file - saves it in the /Report folder
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• Popup Expression Profile plots [CB] - you may adjust the zoom by clicking on the 1X button. Clicking on a sample bar shows what the sample is and its value. Selecting another protein in the scatterplot will change the EP plot.
• Popup scrollable list of EP plots for proteins passing the Filter

• Cluster similar proteins to current protein by EP profile - you must be in 'mean EP-set samples' display mode
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• Use weighted distance metric [RB] - this adjusts the distance taking missing sample values into account (Jain and Dubes)
• Use average all data distance metric [RB] [FUTURE]
• Use Fisher-clustering low values distance metric [RB] [FUTURE]

• Report statistics of proteins passing the filter - the report generated depends on the plot mode and filter options selected
• Report Expression Profiles of proteins passing the filter
• Report X&Y sets statistics of proteins passing missing protein filter
• Report EP set statistics of proteins passing missing protein filter
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• Report list of samples in the current the expression profile
• Report list of all sample assignments
• Report list of # proteins/sample
• Report ProtPlot state
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• Sort report assending order [CB]