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| ====== Worked example Variant Interpreter ====== | ====== 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]]. | **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 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). | + | **2-** We will work with expression data from custom tissue related to Fanconi Anemia (bone marrow derived cells). You can download the raw expression matrix used for this example 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). |
| - | + | Hipathia only takes as input normalized data, so you will have to correctly normalize the raw expression matrix to be uploaded. | |
| - | * Custom tissue expression matrix: {{:brca_genes_vals_bn.txt|}} | + | * 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]]. | **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]]. | ||
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| {{ :variantexample1.png |}} | {{ :variantexample1.png |}} | ||
| - | **4-** We will evaluate the impact of dirsupting variants in genes //BRCA1//, //FANCD2//, //ATR// and //CTNNB1//. 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. | + | **4-** We will evaluate the impact of disrupting variants in gene //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. | **5-** Press the //Variant Interpreter// button. | ||
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| {{ :uploadgenelist.png |}} | {{ :uploadgenelist.png |}} | ||
| - | **7-** (OPTIONAL) Select the GTEx tissues to use ... the //Differential signaling// button. | + | **7-** (OPTIONAL) Select one or more in the GTEx tissues list in order to compare between them. |
| - | {{ :gtex_tissues.png |}} | + | |
| **8-** (OPTIONAL) Select a subset of signaling pathways to evaluate, all pathways are selected by default. | **8-** (OPTIONAL) Select a subset of signaling pathways to evaluate, all pathways are selected by default. | ||
| {{ :pathwayslist.png |}} | {{ :pathwayslist.png |}} | ||
| - | **9-** In the //Job 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 job, for example "FA KO analysis". | + | **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 raw expression matrix used for this example 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 | ||
| + | Hipathia only takes as input **normalized data**, so you will have to correctly normalize the raw expression matrix to be uploaded. | ||
| + | * 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. Each gene list correspond to all the genes that compose a single circuit from related and non related pathways to the disease, circuits are named after their effector node: | ||
| + | * {{ :listagenesKO_diabetesRap1.txt | Gene list for example 1: Rap1 signaling pathway: PRKCI PARD6A PARD3}} | ||
| + | * {{ :listagenesKO_diabetesChemokine.txt | Gene list for example 2: Chemokynes signaling pathway: PARD3-PRKCZ-TIAM1}} | ||
| + | * {{ :listagenesKO_diabetesTNF.txt | Gene list for example 3: TNF signaling pathway:CREB3}} | ||
| + | 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|here]]. 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. | ||
| - | **11-** Press the //Run analysis// button. A job will be created and listed in the jobs panel. You can access this panel by clicking on the //My jobs// button. | ||
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