Differences

This shows you the differences between two versions of the page.

--- workflow [2016/02/08 12:20] – fsalavert
+++ workflow [2017/05/24 15:27] (current) – external edit 127.0.0.1
@@ Line 9: / Line 9: @@
 The upper bar (**1**) includes, from left to right:
-  * The home button
+  * The Jobs button
   * Settings button
   * The user name, once you have already logged in.
@@ Line 16: / Line 16: @@
   * Info, where you can find a link to the documentation of the tool.
-===== 1. Back button =====
+===== 2. Tool buttons =====
-This button allows you to go back to start page, where you can create new jobs or view existing jobs.
+  * Back: Allows you to go back to the jobs view,where you can create new jobs or view existing jobs.
+  * 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.
 ===== 3. Pathway viewer =====
@@ Line 38: / Line 41: @@
-===== 6. Gene List =====
+===== 6. Add genes =====
-The gene list panel includes the //Update// button, the //Search genes// window an the list of genes with modified expression.
+The Add genes panel includes the //Search genes// window and the list of genes with modified expression.
   * **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.
@@ Line 46: / Line 49: @@
   * **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 any of the genes selected in Gene list (**6**). You can simulate the application of any of this drugs by checking their corresponding checkbox.
+===== 9. Genes affected by drugs =====
+The genes affected by drugs (**9**) lists the genes whose expression is being modified by any of the selected drugs in the gene related drugs panel (**7**).
+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.
-{{ :pathact_target_actions.png?600 |}}
-===== 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:
@@ Line 73: / Line 78: @@
 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.
+===== 11. Settings button  =====
-===== ?. Expression matrix panel =====
+In this window you can configure the fold change threshold beyond a circuit is considered statistically significant.
-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.
-You can load different files to work with, and all of them will be listed in the panel, allowing you to use equally one or another. Files can be loaded as:
+Also can configure the effect of each type of drug by clicking on the //Settings// button.
+{{ :settings0.png?600 |}}
-  * **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.
+===== 12. Last update gene list  =====
-  * **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 and organize it as desired. For further information on how to update data to PathAct, see [[Upload your data|Upload your data]].
+This panel shows the last update gene list with it's activity status.
+Last update gene list