Differences

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

--- path_values [2015/12/28 11:03] – mhidalgo
+++ path_values [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== Path values ======
+====== Module Values ======
-Here you will find descriptive information about the matrix of circuit values.
+Here you will find descriptive information about the section of Module Values.
-  * **Circuit values**: You can download the matrix of circuit values by clicking on //Circuit values//.
+  * **Module values**: You can download the matrix of module activity values by clicking on //Module 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.
-  * **Circuit 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:
+  * **Module significance**: Ordered table of module significance. More significant module are displayed in the upper part of the table. For each circuit, the following information is shown:
-    * **circuit/term**: Code identifying the circuit 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.
+    * **ModuleID**: This code is identifying the KEGG module ID and the metabolite which produced (last node of module) by the module (e.g M00036_C00164). If module is a loop like TCA cycle, a random node of the module is used as last node of module (M00009_R00342,R00361).
-    * **UP/DOWN**: Up when the circuit is up-regulated in the disease case, DOWN otherwise.
+    * **ModuleDescription**: Description of the module.
-    * **statistic**: Statistic of the of the statistic test.
+    * **Pathway**: Name of the pathway which contains module.
+    * **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.
+    * **adj.pvalue**: Adjusted p-value of the statistic test using the FDR method.
+    * **Status**: Up when the module is up-regulated in the disease case, DOWN otherwise.
+    * **StartMetaboliteID**: First node(s) of the module. Node(s)with zero indegree. KEGG metabolite ID.
+    * **StartMetaboliteName**: First node(s) of the module. Node(s)with zero indegree. KEGG metabolite name.
+    * **StartMetaboliteID**: First node(s) of the module. Node(s)with zero indegree. KEGG metabolite ID.
+    * **StartMetaboliteName**: First node(s) of the module. Node(s)with zero indegree. KEGG metabolite name.
+    * **EndMetaboliteID**: Last node of the module. Node with zero outdegree. KEGG metabolite ID.
+    * **EndMetaboliteName**: Last node of the module. Node with zero outdegree. KEGG metabolite name.
+    * **KEGGlink**: Link of the module on http://www.genome.jp/kegg/module.html