The resulting network will load automatically. Open the options panel and confirm you are searching Homo sapiens with a cutoff of 0.4 and 0 maximum additional interactors.In the Network Search bar at the top of the Network Panel, select STRING protein query from the drop-down, and paste in the list of up-regulated genes.In Excel, copy the entries in the Gene column to the clipboard. This file contains the subset of genes that were up-regulated in the experiment.Download the list of up-regulated genes, and open it in Excel.The two examples are split into two separate workflows on the following slides. Query STRING disease for a keyword ovarian cancer.Query STRING protein with the list of differentially expressed genes.To identify a relevant network, we will use the STRING database in two different ways: For this workflow, we will use the STRING app. Many public databases and multiple Cytoscape apps allow you to retrieve a network or pathway relevant to your data. Install the stringApp from Apps → App Store → Show App Store. ![]() We will focus on the differential gene expression between two subtypes:įor convenience, the data has already been analyzed and pre-filtered, using log fold change value and adjusted p-value. The data used in this protocol are from The Cancer Genome Atlas, in which multiple subtypes of serous cystadenocarcinoma were identified and characterized by mRNA expression. ![]() Ovarian serous cystadenocarcinoma is a type of epithelial ovarian cancer which accounts for ~90% of all ovarian cancers.
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