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The gene object is a rectangle that contains the label for a gene and links to information about the gene from the Gene Database and Expression Datasets. To add a gene to a MAPP, place it on the Drafting Board as you would other objects. You can move a gene object by left-clicking on it to select it and dragging the edit point that appears at the center of the gene object. You may size the gene object by dragging the edit point on the right edge of the gene. As you drag the edge, the opposite edge moves in the opposite direction, maintaining the location of the center point. The gene label stays centered on the center edit point. A gene object cannot be smaller than the space required to accommodate its label, and it cannot be rotated. The color of a gene object is controlled by the particular Expression Dataset and Color Set currently being viewed on the MAPP. |
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When you place a gene object on the Drafting Board, it has no label, identifier, or data attached to it. One of your first tasks should be to provide this information. Right-click on the gene to open the Gene Finder window. First, fill in the gene identifier, then fill in the rest of the information.
The gene identifier is the link between the gene object and information in the Gene Database and data in your Expression Dataset. You must enter a Gene ID and then select the appropriate Gene ID System from the pull-down menu. For a MAPP to be maximally useful, we are encouraging GenMAPP users to use the ID from the Model Organism Database (MOD) whenever possible (Ensembl is the MOD for all GenMAPP Gene databases except for Yeast, which uses SGD as the MOD). GenBank should not be used as a Gene ID on a MAPP if at all possible. Because of the large number of GenBank IDs in the Gene Database, using GenBank IDs makes coloring MAPPs and running MAPPFinder significantly slower than if the other systems are used.
To assign a gene ID to a gene object, enter the gene identifier, select the appropriate type of identifier you have used from the pull down menu, and click the Search button. GenMAPP will search the current Gene Database for your entry. If it finds it, GenMAPP will fill in the mini-browser area with the relevant information contained in the Gene Database and display Gene Found. The gene IDs in the mini-browser are hyperlinked and will take you to the corresponding page on the public database sites. There are three navigation buttons below the mini-browser, Back, Forward, and Home to assist you in navigation.
If the gene identifier is not found in the Gene Database, a warning will display. Check to see if you typed the identifier correctly and that you have selected the correct Gene ID System. If GenMAPP still cannot find the gene identifier in the Gene Database, you have the option of adding the identifier to your local copy of the Gene Database in the Other table. To do this, enter the gene ID in the Gene ID box, select the Other Gene ID System and click Search. When the dialog box asks you if you want to add the gene to the Gene Database, click yes. Be careful when adding gene identifiers to the Gene Database; they will become a permanent part of your local copy of the Gene Database. An Other gene identifier must be 30 characters or fewer. Commas, quotes (single or double), or the dollar sign may not be used in an Other gene identifier. Other non-alphanumeric characters are allowed. You can also add a gene to the Other category by processing exceptions, or by directly editing the Other table in the Gene Database Manager.
If your gene does not have an ID in any of the available systems and you do not wish to add the ID to the Other category, you can add your own gene ID system to the Gene Database through the Gene Database Manager. You can also add the genes to the Other category, either by processing exceptions, or by directly editing the Other table in the Gene Database Manager. You can also add genes to the Other category through the Gene Finder window, as described above.
You may change the gene identifier of a particular gene on a MAPP at any time.
| Note: When adding genes to the Other category or adding custom gene ID systems via the Gene Database Manager, these new IDs will be colored in GenMAPP if they also exist on a MAPP as well as in an Expression Dataset. |
The gene label is the text you wish to appear within the gene box on the Drafting Board. It will default to the gene identifier. We suggest that you use the standard gene symbol approved by the model organism database (MOD) for each organism to facilitate communication of MAPPs between researchers. The gene symbol from the MOD will appear in the mini-browser. You can copy it from there into the Gene Label field.
Once the identifier for a gene has been entered in the Gene Finder, double-left-clicking on the gene on the Drafting Board brings up a Backpage window that contains the data and annotation associated with that gene. Each Backpage is a separate web page shown in Internet Explorer. You may have many Backpages open at once, allowing you to move back and forth between GenMAPP and each of the Backpages. Be sure to close each of them when you finish with it to avoid screen clutter. These windows will remain open even if you exit the GenMAPP program. Since the Backpage is housed in a web browser, you can click on any of the links or use the browser as you normally would. You must, of course, have an internet connection to utilize any of the links.
Below is an example of what a Backpage might look like:
| Technical Note: Each Backpage generates a separate HTML file, stored in your program path (C:\Program Files\GenMAPP 2 for a default installation) in a subfolder called Backpages. Its title is the heading you entered for the Backpage in the Gene Finder (or the gene label if there is no heading) plus .htm. These files will remain until you start GenMAPP again. |
The Backpage heading is the first line or title of the Backpage. It defaults to the gene label. If you used the gene symbol for the gene label, we suggest that you use the full-length name for the gene or protein for the Backpage Heading.
Text entered into the Backpage Remarks field will appear on the Backpage for that gene below the annotations for that gene from the Gene Database. Since the Backpage is a browser, you may embed any HTML code in your Remarks and they will be displayed on the Backpage. For example, to embed a hyperlink in your Remarks, you may do something like the following:
See <a href="http://www.GenMAPP.org">GenMAPP site</a> for info
Click the OK button to save the information and close the Gene Finder window. You may edit any of these fields by right-clicking on the gene object on the Drafting Board again.
When a gene object is initially placed on the Drafting Board, its background color will be white. Genes have a background color other than white only when data from an Expression Dataset has been applied to the MAPP. Criteria for coloring gene objects may be determined in the Expression Dataset Manager. You can color genes on a MAPP with different Expression Datasets by choosing Data > Choose Expression Dataset, from the menu at the top of the Drafting Board window. You may switch between different Color Sets for the same Expression Dataset using the Color Set pull-down menu on the Drafting Board Toolbar.
Each time you choose a Color Set, GenMAPP automatically applies the expression data to the genes on the Drafting Board according to the Criteria you have set in the Expression Dataset Manager. The criterion that is met by the data for the gene in the Expression Dataset determines the color of the gene rectangle and the Gene Value displayed on a MAPP. A dashed line around the gene rectangle indicates the existence of duplicate data. If the gene rectangle with a dashed line is filled with two different colors (a central color and a rim color) that means that two different lines of data associated with that gene object meet different criteria in the Color Set. The central color is determined by the most frequent criterion met (the mode) by the data corresponding to that gene object. The rim color is determined by the next most frequent criterion met by the data corresponding to the gene object. Double-left-click on a gene rectangle on a MAPP to open the Backpage and view all the data along with the corresponding gene identifiers. Double-left-click on a gene rectangle on a MAPP to open the Backpage and view all the data along with the corresponding gene identifiers.
You may return the genes on a MAPP to white by selecting No expression data from the Color Set pull-down menu in the Drafting Board Toolbar.. If you add a new gene object to a MAPP that has already been colored with an Expression Dataset, you may color the new gene by selecting Data > Apply Expression Data. If the gene object remains white after you have applied the data, it means that gene identifiers corresponding to that particular gene object do not exist in the Expression Dataset chosen for display.
The gene values are taken from your chosen column in your Expression Dataset. The value will be shown to the right of the gene rectangle. Gene values are limited to six characters, including a decimal point for numerical values (e.g., 37.524 or –98763), or six characters for character data (e.g., kinase). Very large or small numbers are displayed in exponential notation. GenMAPP will always need room for the gene value, so do not put any other objects or lines close to the right of a gene rectangle.
The label tool is used to place and edit text on the Drafting Board. To create a label, place it on the Drafting Board as you would other objects. To edit the label, right-click on it. A Label Data window will open where you may type the text you wish to appear on the Drafting Board in the label field. Click OK to save the changes made and return to the Drafting Board window. If you click the cancel button or close button in the title bar of the Label Data window, you will be returned to the Drafting Board without saving the changes.
To change the font, style, size, or color of the label, click the Font button and make the desired changes in the Font window that appears. Be careful when choosing a font other than the default (Arial) for a label. Some fonts may not display well on your printer or when the file is exported. Click OK to return to the Label Data window, and cancel to return without saving the changes.
Notes typed in the Notes field of the Label Data window can only be accessed from this window.
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To add a rectangle to a MAPP, place it on the Drafting Board as you would other objects. To move, size, or rotate a rectangle, left-click on the edge to select it. If you are having trouble selecting a rectangle, try double-clicking on the very edge. Drag the center point to move it, the right edge point to adjust the width, the bottom edge point to adjust the height, or the circular point to rotate it. If you hold down the shift key while dragging either of the sizing (edge) points, the rectangle will become a perfect square, its size set by the point you dragged. Holding the shift key while dragging the circular point rotates the rectangle to the nearest 45º angle. You can fill the rectangle by right-clicking on the edge of the rectangle and then picking a color from the Color window that appears. Once filled, a rectangle may not be returned to transparent (even white is a solid fill); to change it back, delete the rectangle and draw another one without filling it. |
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To add an oval to a MAPP, place it on the Drafting Board as you would other objects. To move, size, or rotate an oval, left-click on the edge to select it. If you are having trouble selecting an oval, try clicking on the very edge. Drag the center point to move it, an edge point to elongate it on either axis, or the circular point to rotate it. If you hold down the shift key while dragging either of the sizing (edge) points, the oval will become a perfect circle, its size set by the point you dragged. Holding the shift key while dragging the circular point rotates the oval to the nearest 45º angle. To fill the oval, right-click on the edge of the oval and pick a color from the Color window that appears. Once filled, an oval may not be returned to transparent (even white is a solid fill); to change it back, delete the oval and draw another one without filling it. |
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Lines, arrows, receptors, ligands, and the inhibition symbol, collectively referred to as line tools, all work similarly. To choose one from the Drafting Board Toolbar, left-click on the drop-down arrow next to the icon. After you have chosen the tool, left-click on the Drafting Board, this first click sets one end of the line—in all cases the plain end. A second left-click sets the arrow, receptor, ligand, T end, or simply the other end of a line. Line tools are adjusted by moving each of the end points. Left-click on or near the line and two red targets appear at either end of the line. Drag either target to a new location and when you drop it, the line will end at that new location. Hint: to move a line tool without changing its length or orientation, left-click on it while holding down the Control key. The line tool can then be moved like a multiply selected object. |
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To add a note to a line tool, right-click on it and fill in the text box.
From this window you can also choose a color by clicking on the Color button. This note is stored with the line and appears if you right click on it again. This note can be used to add annotation to the line such as the meaning (activation, inhibition, binding, indirect interaction, etc.) and/or a reference.
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Ligands and receptors work similarly to other line tools. To choose one from the Drafting Board Toolbar, left-click on the drop-down arrow next to the icon. Set the plain end first, and then the receptor or ligand end. To allow for correct spacing between ligands and their receptors, the red target box on the ligand end point is meant to coincide with the end point on the receptor; (i.e., it is beyond the actual ligand end point). Hint: to assure that the line is straight through both the ligand and receptor, you may want to draw a straight line and use it to locate the ligand/receptor points. Be sure to make the temporary line longer than the ligand/receptor pair so that you can select the line to delete it. To add a note to a ligand or receptor, right-click on it and fill in the text box. From this window you can also choose a color by clicking on the Color button. This note is stored with the line and appears if you right click on it again. This note can be used to add annotation to the line such as the meaning (activation, inhibition, binding, etc.) and/or a reference. |
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Curves are drawn like ovals. To add an curve to a
MAPP, place it on the Drafting Board as you would other objects.
Left-click on a curve to select it. To move, size, or rotate a curve,
left-click on the edge to select it. If you are having trouble
selecting an oval, try clicking on the very edge.
Drag the center point to move it, an edge point to elongate it on
either axis, or the circular point to rotate it. If you hold down the
shift key while dragging either of the sizing (edge) points, the oval
will become a perfect circle, its size set by the point you dragged.
Holding the shift key while dragging the circular point rotates the curve
to the nearest 45º angle. To add a note to a curve, right-click on it and fill in the text box. From this window you can also choose a color by clicking on the Color button. This note is stored with the line and appears if you right click on it again. This note can be used to add annotation to the line such as the meaning (activation, inhibition, binding, etc.) and/or a reference. Hint: to make a curved arrow, place a curve in the position desired. Then make a very short arrow with the arrow tool. Position the arrowhead at the end of the curve. |
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Braces are placed on the Drafting Board like other objects. The point at the center of the brace will appear where you position the crosshair. A brace is initially set at a top orientation and a preset span which you can change by left-clicking on the brace to select it. To move a brace, drag the center target to a new location on the Drafting Board. Dragging the target at the end of the brace increases or decreases its span. Notice that it will only move in line with the brace. When you drop it, the other end will automatically adjust to whatever length you have set for the target end, maintaining the center point in place. Braces may be rotated to any one of four orientations, left, right, top, and bottom. The circular target at the other end of the brace rotates it. Your setting is adjusted to the nearest 90º. To change the color of a brace right-click on it and choose a color from the Color window that appears. |
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The Color Set drop-down list displays all Color Sets in the current Expression Dataset. Click on the arrow to show the Color Sets.
To select a single Color Set, left-click on that Color Set in the list.
To select multiple Color Sets in the Color Set drop-down list, left-click the Multiple Color Sets option in the Choose Color Set list. A window for selecting Color Sets will appear.
To select multiple Color Sets, hold down the Ctrl key and select the appropriate Color Sets in the left panel. To select all Color Sets, left-click the All button.
To select which from which Color Set to choose a Display Value, select a Color Set in the right panel. It is possible to select any Color Set at this point, regardless of which Color Sets where selected for coloring. The gene value does not have to correspond to the Color Set selected for display. There is also an option for not displaying gene values next to the gene box.
If multiple Color Sets are chosen for display, the gene boxes on the MAPP will be partitioned into colored stripes, each representing a selected Color Set.
For details on how to interpret the display of multiple Color Sets, see the Legend section.
The Zoom drop-down menu allows you to quickly access the Zoom function.
