CoV-HiPathia

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====== Worked example Variant Interpreter ====== ===== Example 1: Fanconi Anemia study ===== **1-** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]]. **2-** We will work with expression data from custom tissue related to Fanconi Anemia (bone marrow derived cells). You can download the expression matrix to be uploaded from GEO repository, accession number [[https://www.ncbi.nlm.nih.gov/pubmed/19850743|GSE16334]]. You can read the original study here: Vanderwerf et al. TLR8-dependent TNF-(alpha) overexpression in Fanconi anemia group C cells. Blood. 2009 Dec 17;114(26):5290-8). * Custom tissue expression matrix after normalization: {{:onlyCexpreset_hinorm.txt|FA expression matrix}} **3-** Upload the data to HiPathia in the data panel by clicking on //My data//. For further information on this step visit [[upload_your_data|Upload your data]]. {{ :variantexample1.png |}} **4-** We will evaluate the impact of disrupting variants in genes //BRCA1// (Biallelic BRCA1 mutations are regarded either embryonically lethal or to cause Fanconi anemia (FA), a genomic instability syndrome characterized by bone marrow failure, developmental abnormalities, and cancer predisposition [[[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6732317/ | cita ]]] ). We need to upload the list of genes in txt format the same way we did to upload expression data. Both gene names and entrez ids are accepted. Select Gene list as data type. **5-** Press the //Variant Interpreter// button. {{ :variantinterbtn.png |}} **6-** In the //Input data panel//. Press the //File browser// and select the desired file for gene list and custom tissue expression file (OPTIONAL). {{ :uploadgenelist.png |}} **7-** (OPTIONAL) Select one or more in the GTEx tissues list in order to compare between them. **8-** (OPTIONAL) Select a subset of signaling pathways to evaluate, all pathways are selected by default. {{ :pathwayslist.png |}} **9-** In the //Study information// panel, press the //File browser// button and select the desired output folder. In this case we will use //FA_KO_analysis//. Give a name to the study, for example "FA KO analysis". {{ :studyinfovafin.png |}} **10-** Press the //Run analysis// button. A study will be created and listed in the studies panel. You can access this panel by clicking on the //My studies// button. ===== Example 2: Diabetes study ===== **1-** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]]. **2-** We will work with expression data from custom tissue related to Diabetes. You can download the expression matrix to be uploaded from GEO repository, accession number [[https://www.ncbi.nlm.nih.gov/pubmed/22768844|GSE38642]] You can read the original study here: https://www.ncbi.nlm.nih.gov/pubmed/22768844 * Custom tissue expression matrix after normalization: {{:onlyCexpresetDiabetes.txt|Diabetes expression matrix}} **3-** Upload the data to HiPathia in the data panel by clicking on //My data//. For further information on this step visit [[upload_your_data|Upload your data]]. **4-** We will evaluate the impact of disrupting variants in each gene **independently** of these gene lists: * {{ :listagenesKO_diabetesRap1.txt | Example 1: Rap1}} * {{ :listagenesKO_diabetesChemokine.txt | Example 2: Chemokine}} * {{ :listagenesKO_diabetesTNF.txt | Example 3: TNF}} After choosing one or more from the studied example and prepare a list of gene(s) in txt format as described [[gene_list_file_format|her]]. We need to upload it the same way we did to upload expression data. Both gene names and entrez ids are accepted. Select Gene list as data type. **5-** Press the //Variant Interpreter// button. {{ :variantinterbtn.png |}} **6-** In the //Input data panel//. Press the //File browser// and select the desired file for gene list and custom tissue expression file (OPTIONAL). {{ :uploadgenelist.png |}} **7-** (OPTIONAL) Select a subset of signaling pathways to evaluate, all pathways are selected by default. {{ :pathwayslist.png |}} **8-** In the //Study information// panel, press the //File browser// button and select the desired output folder. In this case we will use //Diabetes_KO_analysis//. Give a name to the study, for example "Diabetes KO analysis". **9-** Press the //Run analysis// button. A study will be created and listed in the studies panel. You can access this panel by clicking on the //My studies// button.