Differences

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

--- differential_signaling [2021/01/27 15:22] – jdopazo
+++ differential_signaling [2021/01/29 22:14] (current) – [Differential signaling form] krian
@@ Line 9: / Line 9: @@
 {{ :differential_signaling_form.png?nolink |}}
 ===== Differential signaling form =====
-The main page of the tool is its filling in form. This form includes all the information and parameters that the tool needs to process a Differential signaling study. The form is divided in different panels:
+The main page of the tool is its filling form. This form includes all the information and parameters that the tool needs to process a Differential signaling study. The form is divided into different panels:
 ==== Input data panel ====
 In the input data panel, we must introduce the expression data.
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 {{ ::pathwaysreport1.png?nolink |}}
   - In the upper-right part of the visualization tool, all selected pathways from the differential signaling form are shown along with one or two arrows. These arrows indicate whether in one of the "Effector circuit" within each pathway a differential activation pattern between the two compared groups have been found.\\ The arrows will be colored if the differential activation is significant after the p-value adjustment (or unadjusted p-value, if the "Unadjusted" parameter has been selected) and depicted in grey if it isn't.\\ The arrow will point up or down if an up-regulation or down-regulation of the signal occurs between the circuits within that pathway.\\ The meaning of this up or down-regulation depends on the comparison performed, that normally would be case vs. control (comparison between selected class from the design file : condition 1 Vs condition 2).\\ Only one arrow is shown if all the effector circuits are whether up or down-regulated.{{ ::pathwaysreport2.png?nolink |}}
-  -  In the lower-right part of the tool will appear all the circuits in which a pathway (previously selected on the upper part -1-) can be decomposed. Once any of the circuit is clicked the nodes and interactions (edges) that form part of this circuit are highlighted in the pathway viewer (), One example might be the red-highlighted circuit on the figure below.{{ ::effectorcircuithl.png?nolink |}}
+  -  In the lower-right part of the tool will appear all the circuits in which a pathway (previously selected on the upper part -1-) can be decomposed. Once any of the circuit is clicked the nodes and interactions (edges) that form part of this circuit are highlighted in the pathway viewer, One example might be the red-highlighted circuit on the figure below.{{ ::effectorcircuithl.png?nolink |}}
   - In the visualization part there are two types of objects, the nodes and the edges.{{ ::pathwaysreport3.png?nolink |}}
     * The nodes represent the different proteins or metabolites that are responsible of the transduction of the signal from the previous node to the next one. As commented before, the nodes can be plain or complexes. In the former it is only necessary the presence of one protein (although that same function can be done by several proteins), while in the complex ones it is necessary the presence of two or more proteins to pass the signal through.\\ The color on the nodes are the result of a differential expression analysis on the gene/s involved on performing that node's function.