vafin
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vafin [2020/02/06 14:19] krian [Variant interpreter report] |
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. | ||
| - | {{ ::compairingtissue.mp4 |}} | + | {{ ::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 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.1580998775.txt.gz · Last modified: 2020/04/03 20:18 (external edit)
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