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| + | This page has been retired, current tutorial content is available [[Help:Tutorial|here]]. |
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| - | {{Template:TutorialNavigate|5}}
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| - | ==Illustrate the E-box enhancer==
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| - | {{TutorialVideo|R3_gF30lVXk|360|Drawing the E-box element}}
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| - | Target genes of the circadian clock pathway contain the E-box ''cis''-regulatory enhancer elements. The Bmal1/Clock heterodimer directly activates expression of these genes by binding to the E-box sequence. In this section we are going to draw an illustration of this process. It will become a purely visual element of the pathway, so it's not annotated to any biological database and will be added for illustrational purpose only.
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| - | {{TutorialHint|In this tutorial and on WikiPathways, you will see many elements in a pathway that have a clearly defined biological meaning and could be annotated to an external database. Examples are genomic sequences, SNPs, cellular locations, interaction types. We are working on supporting these kinds of annotations in future releases.}}
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| - | The video on the right shows how to draw the E-box element, which in the end will look like this:
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| - | {|class=prettytable
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| - | |{{TutorialImage|e-box.png}}
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| - | |}
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| - | Below is a step-by-step description of how to create such an element:
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| - | ==== 1. Draw a horizontal line ====
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| - | Start with a horizontal line, by clicking the {{TutorialImage|newlinemenu.gif}} ''line dropdown menu'' and selecting the ''line'' button. Next, move to the location on the drawing where you want the line to start. Press down the mouse button, drag the mouse to the right (while holding the button down!) and release the button at the location where you want the line to end. You can modify the location of the start and end points by dragging the handles (yellow squares). You can modify the location of the whole line by clicking on the line itself and dragging it.
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| - | {{TutorialHint|You can easily make a perfectly horizontal or vertical line by holding the Shift button on you keyboard while moving a line end. This will snap the line fixed angles.}}
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| - | ==== 2. Copy/paste the line ====
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| - | We now want a second horizontal line of the same length and parallel to the first line. Therefore, we are going to copy the line from the previous step. Select the line by clicking on it, the line will turn red and the two handles will be visible. Now click the {{TutorialImage|copy.gif}} ''copy'' button. The line is now copied to your system's clipboard. You can paste a copy of the line by pressing the {{TutorialImage|paste.gif}} ''paste'' button. A copy of the line now appears a little below the original line.
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| - | ==== 3. Align the two lines vertically ====
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| - | To put the lines exactly below each other, select both lines and press the {{TutorialImage|aligncenterx.gif}} ''align horizontal center'' button. You can select multiple objects by pressing the mouse on an empty part of the drawing, hold the mouse button down and drag the mouse to include or exlude elements from the selection. You can also select or deselect multiple objects by clicking them while holding the ''Shift'' button on your keyboard.
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| - | ==== 4. Draw a label ====
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| - | Now we have two parallel horizontal lines that represent a piece of DNA. We can denote the E-box region by placing a label over the lines. Add a label using the {{TutorialImage|newlabel.gif}} ''label'' button.
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| - | ==== 5. Set the label text to 'E-box' and apply the 'square' outline ====
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| - | Label properties can be edited in the ''Properties table''. Set the property ''Text Label'' to 'E-box' by double clicking on the cell in the ''Value'' column:
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| - | {|class=prettytable
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| - | |{{TutorialImage|textlabel.png}}.
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| - | |}
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| - | In the same way, you can set a rectangular outline, by selecting the 'Rectangle' for the ''Outline'' property. Finally, use the handles to resize the label so that it exactly fits between the two horizontal lines.
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| - | ==== 6. Copy/paste the label and change text to 'Gene' ====
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| - | Downstream of the E-box element is the gene that will be activated. We can denote this with a label too. Copy/paste the E-box label and change the text to 'Genes', since we use a single element to depict multiple genes that will be activated. Drag the label to put it at the right position.
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| - | ==== 7. Draw a transcription start symbol ====
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| - | To make it clear that the genes downstream of the E-box element are transcribed after activation, the following symbol is used:
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| - | {|class=prettytable
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| - | |{{TutorialImage|transcription.png}}
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| - | |}
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| - | This symbol is made out of a vertical line and horizontal arrow. Draw the line and arrow by using the {{TutorialImage|newline.gif}} ''line'' and {{TutorialImage|newarrow.gif}} ''arrow'' buttons and correctly place them by dragging the handles.
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| - | ==== 8. Group all lines and labels ====
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| - | To make it more easy to handle the E-box illustration, you can group it. This way the elements will be selected together, so you can move the group as a whole, instead of having to move each element separately. To create the group, select all lines and labels you created in the previous steps, right-click on one of the lines and select ''Group->Group'' from the pop-up menu, or press ''CTRL-G'' on the keyboard. You can ungroup the grouped elements by right-clicking the group and selecting ''Group->Ungroup'', or pressing ''CTRL-G'' again.
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| - | {{Template:TutorialNavigate|5}}
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