Differences

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

--- differential_signaling [2015/12/28 11:03] – mhidalgo
+++ differential_signaling [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== Differential signaling ======
+===== Module Activity =====
-HiPathia allows us to compute a signal value for each signaling path and each one of our data samples.
+Metabolizer allows us to compute activity value for each module and each one of our data samples.
-Therefore, it allows us to compare the signal value between different conditions.
+Therefore, it allows us to compare the module activity value between different conditions.
-Depending on the available input data, different comparisons can be performed:
+The tool can be accessed from the main menu bar, by clicking on the //Activity// button, see [[workflow|Workflow]] for further information.
-  * **Only expression**: we can compare either two groups or correlate the path value with a continuous variable.
-  * **Only VCF**: we can compare either two groups or correlate the path value with a continuous variable.
-  * **Expression + VCF**: apart from comparing two groups and correlating the path value with a continuous variable, we can also check the effect of the mutations in the signals of each sample.
-The tool can be accessed from the main menu bar, by clicking on the //Differential signaling// button, see [[workflow|Workflow]] for further information.
  === INPUT ===
@@ Line 17: / Line 12: @@
   * [[Design data|Design data]]
   * [[Species|Species]]
-  * [[Mutation effect|Mutation impact]]
-  * [[Parameters|Parameters]]
-  * [[Function level analysis|Function level analysis]]
-  * [[Pathways|Pathways]]
   * [[Job information|Job information]]
@@ Line 27: / Line 18: @@
 === OUTPUT ===
-The results page of the Differential signaling tool includes different output results. You can download any table or image showed in the results page by clicking on the name right before it. You can also download the pathway and function matrices by clicking on //Path values//, //GO terms values// and //Uniprot keywords values// respectively.
+The results page of the module activity tool includes different output results. You can download any table or image showed in the results page by clicking on the name right above it. You can also download calculated module activity values and statistical results by clicking on //**Module values**// and //**Path significance**// respectively. Using module activity values clustering of the samples are represented with heatmap and Principal component analysis (PCA) plots
 The results are divided in different panels:
   * [[Input Parameters|Input Parameters]]
-  * [[Path values|Circuit values]]
+  * [[Path values|Module Values]]
-  * [[Function based analysis|Function based analysis]]
   * [[Pathway viewer|Pathway viewer]]