vafin
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vafin [2020/02/06 14:10] krian [Visualization part] |
vafin [2020/04/03 20:18] (current) |
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| {{ ::checkedsearchforcustomtissue.png?nolink |}} | {{ ::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 minutes depending on you custom tissue file 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 ==== | ==== 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. | 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. | ||
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| ===== Variant interpreter report ===== | ===== 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. | 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. | ||
| - | {{ ::vafinpthvw.png?nolink |}} | + | {{ ::compairingtissueprec.mp4?nolink&900 |}} |
| This interactive working environment is divided in different panels: | This interactive working environment is divided in different panels: | ||
| ==== Tissue list ==== | ==== Tissue list ==== | ||
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| * 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. | * 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 ==== | ==== 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. | 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: | Also you can find other button in the right side: | ||
| - | * {{::search.png?nolink|}}Allow to search specific genes, proteins or functions.{{ ::searchapoptosis2.mp4?nolink&600 |}} | + | * {{::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) | * {{::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 | * {{::center.png?nolink|}}Center the selected pathway | ||
vafin.1580998203.txt.gz · Last modified: 2020/04/03 20:17 (external edit)
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