workflow
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| workflow [2016/02/08 12:16] – fsalavert | workflow [2017/05/24 15:27] (current) – external edit 127.0.0.1 | ||
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| ====== Structure & Workflow ====== | ====== Structure & Workflow ====== | ||
| - | {{ : | + | {{ : |
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| The upper bar (**1**) includes, from left to right: | The upper bar (**1**) includes, from left to right: | ||
| - | * The home button | + | * The Jobs button |
| * Settings button | * Settings button | ||
| * The user name, once you have already logged in. | * The user name, once you have already logged in. | ||
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| * Info, where you can find a link to the documentation of the tool. | * Info, where you can find a link to the documentation of the tool. | ||
| - | ===== 2. Expression matrix panel ===== | + | ===== 2. Tool buttons |
| - | + | * Back: Allows | |
| - | In the expression matrix panel (**2**) you can upload the expression matrix you are interested in working with. Only the first column of the data matrix will be considered. | + | * Update: When genes are selected, it will update the pathways with the selected expression. |
| - | + | * Clear: Removes all genes and updates the pathways with the initial values. | |
| - | You can load different files to work with, and all of them will be listed in the panel, allowing | + | |
| - | + | ||
| - | * **Load example file**: An example data set will be loaded, consisting in a unique sample of a Breast Cancer cohort taken from The Cancer Genome Atlas repository. | + | |
| - | * **Load file**: Allows you to upload a file from your computer. The data is arranged in folders as in a personal computer. You can upload data to any folder | + | |
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| - | ===== 6. Gene List ===== | + | ===== 6. Add genes ===== |
| - | The gene list panel includes | + | The Add genes panel includes the //Search genes// window |
| * **Update**: Each time you press the button //Update//, a comparison between the signaling values of the pathways in the current sample and the signaling values resulting from the modification of the expression values in the current sample by the selected values is performed. The results of this comparison can be visualized in the Pathway viewer panel (see [[Results|Results]]) and by pressing the //Show last update report// button. | * **Update**: Each time you press the button //Update//, a comparison between the signaling values of the pathways in the current sample and the signaling values resulting from the modification of the expression values in the current sample by the selected values is performed. The results of this comparison can be visualized in the Pathway viewer panel (see [[Results|Results]]) and by pressing the //Show last update report// button. | ||
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| * **Modified genes list**: List of the genes whose expression has been modified, together with the new value of their expression. In order to remove a gene from the list, press the **x** button next to its expression. | * **Modified genes list**: List of the genes whose expression has been modified, together with the new value of their expression. In order to remove a gene from the list, press the **x** button next to its expression. | ||
| + | ===== 7. Gene related drugs ===== | ||
| - | ===== 7. Additional drug targets ===== | + | The related drug list panel (**7**) lists the drugs including as target any of the genes selected in Add genes (**6**). You can simulate the application of any of this drugs by checking their corresponding checkbox. |
| - | The Additional drug targets list (**7**) lists the genes whose expression is being modified by any of the selected drugs in the Related drug list panel (**8**). | ||
| - | Further information on the kind of drug is also displayed in the list. | + | ===== 8. Add Drugs ===== |
| + | The add drugs panel (**8**) allows to search and add drugs directly. | ||
| - | ===== 8. Related drug list ===== | ||
| - | The related drug list panel (**8**) lists the drugs including as target | + | ===== 9. Genes affected by drugs ===== |
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| + | The genes affected by drugs (**9**) lists the genes whose expression is being modified by any of the selected | ||
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| + | Further information on the kind of drug is also displayed in the list. | ||
| - | You can configure the effect of each type of drug by clicking on the //Configure target actions// buttons. | ||
| - | {{ : | ||
| - | ===== 9. Show report button ===== | + | ===== 10. Show report button ===== |
| The //Show last update report// button shows a new window with the report of the results for the current comparison. This report includes two fields: | The //Show last update report// button shows a new window with the report of the results for the current comparison. This report includes two fields: | ||
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| In order to close this window and return to the tool page, you can press the **x** button on the right upper side of the window. | In order to close this window and return to the tool page, you can press the **x** button on the right upper side of the window. | ||
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| + | ===== 11. Settings button | ||
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| + | In this window you can configure the fold change threshold beyond a circuit is considered statistically significant. | ||
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| + | Also can configure the effect of each type of drug by clicking on the // | ||
| + | {{ : | ||
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| + | ===== 12. Last update gene list ===== | ||
| + | This panel shows the last update gene list with it's activity status. | ||
| + | Last update gene list | ||
workflow.1454933761.txt.gz · Last modified: 2017/05/24 15:27 (external edit)