CoV-HiPathia

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====== Variant Interpreter ====== The Variant interpreter allows us to infer how a gene (or combination of genes) knockdown may deregulate the signaling pathways activity. This impact is evaluated by comparing the normal activity values from a given tissue, with the activity values of that same tissue calculated after the //in silico// knockdown of the expression values of the genes of interest. This can be done for each signaling pathwat and for each one of the tissues included in GTEx. Additionally, the user can upload a file with gene expression data to perform the analysis on custom tissue. Essentially, we are comparing pathway activities between two groups (Normal tissue Vs Knockdown tissue), to aid us in the functional interpretetion of disruptive genomic variants. The tool can be accessed from the upper main menu bar, by clicking on the //Variant interpreter// button. See [[workflow|Workflow]] for further information. {{ :vafin_form.png?nolink |}} ===== Variant interpreter 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 carry out the analysis. The form is divided in different panels: ==== Input data panel ==== {{ ::inputdatavafinform.png?nolink |}} A tabulated text file with data on genomic variation must be uploaded. This file must include list of gene names in HUGO or entrez id (see [[http://hipathia.babelomics.org/doc/doku.php?id=gene_list_file_format|gene list file forma]]t for more information).This genes list corresponds to the genes to in silico knockdown simultaneously.\\ 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 |}} ==== Pathways ==== * [[Pathways|Pathways]] ==== Study information ==== * [[Job information|Job information]] Once the form has been filled in, press the //Run analysis// button to launch a study. Your job will be listed in the //My studies// panel, see [[workflow|Workflow]] for further information. ===== Variant interpreter report ===== The results page of the Variant Functional Interpreter tool ........ You can download the pathway. * [[Pathway viewer|Pathway viewer]]