Differences

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

--- path_values [2015/12/21 17:14] – mhidalgo
+++ path_values [2019/09/01 13:46] (current) – krian
@@ Line 1: / Line 1: @@
-====== Path values ======
+====== Circuit values ======
-Here you will find descriptive information about the matrix of pathway values.
+Here you will find descriptive information about the matrix of circuit/path values.
-  * **Path values**: You can download the matrix of path values by clicking on //Path values//.
+  * **Path values**: You can download the matrix of circuit values by clicking on //Path values//.
   * **Heatmap**: A heatmap is a graphical representation of the values of a matrix. A not-supervised clustering is performed on the data per columns (samples). A good separation between the two colors of the upper bar of the heatmap indicates that the differences between the two groups are big enough to discriminate between them.
   * **PCA**: A Principal Components Analysis is performed in order to see if the matrix contains information enough to separate between the two groups.
-  * **Path significance**: Ordered table of pathway significance. More significant pathways are displayed in the upper part of the table. For each pathway, the following information is shown:
+  * **Path significance**: Ordered table of circuit significance. More significant circuits are displayed in the upper part of the table. For each circuit, the following information is shown:
-    * **path/term**: Code identifying the path consisting in the name of the pathway to which it belongs, the initial node (if //Decompose paths// option was selected) and the effector (last) node of the path.
+    * **circuit/term**: Code identifying the circuit consisting in the name of the pathway to which it belongs and the effector (last) node of the path (//pathway Name : Effector//).
-    * **UP/DOWN**: Up when the path is up-regulated in the disease case, DOWN otherwise.
+    * **UP/DOWN**: Up when the circuit is up-regulated in the disease case, DOWN otherwise.
-    * **statistic**: Statistic of the of the statistic test.
+    * **statistic**: Statistic of the Wilcoxon test performed between conditions.
     * **p.value**: P-value of the statistic test.
     * **FDRp.value**: Adjusted p-value of the statistic test using the FDR method.
+    * **Fold Change**: is a measure describing how much the ** circuit activity** changes between conditions.[[https://en.wikipedia.org/wiki/Fold_change|reed more about Fold Change]]
+    * **logFC**: The logarithm to base 2 of calculated Fold change.