Differences

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

--- vafin [2020/02/05 17:26] – [Run analysis] krian
+++ vafin [2021/01/07 19:23] (current) – [Pathway viewer header] krian
@@ Line 15: / Line 15: @@
 Then you have to select at least one tissue, or a custom matrix file has to be loaded after checking the "Search for custom tissue" checkbox as shown below:
 {{ ::checkedsearchforcustomtissue.png?nolink |}}
-**Note**: You can select all options, but you have to take into account that the analysis will take more minutes depending on you custom tissue file and the server availability.
+**Note**: You can select all options, but you have to take into account that the analysis will take more time depending on your custom tissue file, selected tissues and the server availability.
+When you select the custom gene expression file, the number of samples of this matrix will appear under the “File browser” button as shown below.
+{{ ::customnumsamples.png?nolink |}}
 ==== Pathways ====
 This panel includes the list of all available pathways in HiPathia. We can select the pathways with which the analysis will be performed.\\ HiPathia retrieves pathway information from [[https://www.kegg.jp/kegg/pathway.html|KEGG database]]. KEGG pathway database is a collection of manually drawn pathway maps representing the knowledge on the molecular interaction, reaction and relation networks.
@@ Line 41: / Line 43: @@
 ===== Variant interpreter report =====
+The results page of the Variant Functional Interpreter tool is an **interactive working environment**. You can simulate knockdown of one or several genes in the activity of signaling pathways. Essentially, it is comparing pathway activities between two groups (Normal tissue Vs Knockdown tissue), also you can study the effect of a Knockdown for several tissues simultaneously and compare between them.
+{{ ::compairingtissueprec.mp4?nolink&900 |}}
+This interactive working environment is divided in different panels:
+==== Tissue list ====
+A list with selected tissues from GTEx. If the user uploaded a file with gene expression data a custom tissue will appear in this list under the name "Custom". \\ {{ ::vafinpthvw1.png?nolink |}}
+==== Pathway list ====
+In this part of the visualization tool, all selected pathways from the variant interpreter 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  (Normal tissue Vs Knockdown tissue).\\ The arrows will be colored if the differential activation is significant after the p-value adjustment (calculated from the circuit activity values using Wilcoxon test for paired data) 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.\\ Only one arrow is shown if all the effector circuits are whether up or down-regulated.\\ {{ ::vafinpthvw2.png?nolink |}}
+==== Circuits list ====
+In the lower-right part of the tool will appear all the circuits in which a pathway (previously selected on the upper part -2-) can be decomposed.
+{{ ::vafinpthvw3.png?nolink |}}
+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 blue-highlighted circuit on the figure below.
+{{ ::vafinreport1circuit.png?nolink |}}
+==== Visualization part ====
+In the visualization part there are two types of objects, the nodes and the edges.
+{{ ::vafinpthvw4.png?nolink |}}
+  * The nodes represent the different proteins or metabolites that are responsible on passing the signal from the previous node to the next one. 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.\\ **Note**: In this tool, you will see just the blue color, because of the effect of the in silico knockdown of the expression values of the genes of interest.
+  * The edges represent how the interactions between the different nodes are.\\ If the edge is an arrow then the previous node will be activating the next one, while if it ends with a vertical bar is the former node will inhibit the functionality of the following node. This interactions may be depicted in red or blue depending on the circuit they form part of (whether they are up-regulated or down-regulated). It may occur, that two or even three colors for a same edge are shown, but this only happens when a circuit is not yet selected on the lower-right part of the tool.\\ Once an certain circuit is selected all its edges will be colored in the same color depending on the result of the differential signaling activation analysis between the Normal tissue Vs Knockdown tissue.
+==== Pathway viewer header ====
+{{ ::vafinpthvw5.png?nolink |}}
+The top part contains the title of selected pathway,by clicking on this button {{::keggsource.png?nolink|}} you can see the original source of this pathway.
+Also you can find other button in the right side:
+  * {{::search.png?nolink|}}Allow to search  specific genes, proteins or functions.
+  * {{::export.png?nolink|}}Export a SVG image of viewed objects (the whole pathway or just the selected effector circuit)
+  * {{::center.png?nolink|}}Center the selected pathway
+  * {{::width.png?nolink|}}Width adjust
+  * {{::height.png?nolink|}}Height adjust
+**The Hipathia web version 1.7.2**
+In this version, we have added new options to the pathway viewer as shown in the following image:
+{{ ::vafinpthvw5pv_header.png?nolink |}}
+  * Export: you can export the selected pathway as a SIF or SVG image, also you can export the node and the attributes files.
+{{ ::export_files.png?nolink |}}
+  * Select: you can select by nodes or edges using specific filters and conditions, in the following video you will find an example of looking for the Entrez id "6494" in the gene lists of the selected pathway:
+{{::selectbynode.mp4?900|}}
+you can also select all nodes, first neighbourhood nodes or Invert node selection...as well as edges, or even select everything showed in the pathway viewer.
+  * Visualization: Sometimes we need to export the result, as an image for example, but with personalized details such as colors, sizes, or shapes... you can change its before exporting your personalized layout for further uses.
+{{ ::visualization.png?nolink |}}
+  * Save layout: when you want to keep your actual layout for next use, you can click the //save layout// {{::savelayout.png?nolink|}} button and it will be saved in your session/study folder.
+  * Change the color of the background: you can also change the color of the background as  is shown in the followed tutorial
+{{::changebackground.mp4?900|}}
-The results page of the Variant Functional Interpreter tool ........ You can download the pathway.
-  * [[Pathway viewer|Pathway viewer]]