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Cytoscape huge networks12/13/2022 ![]() ![]() The resulting network will load automatically, and should have around 173 nodes. Click Import to continue with the import using the default choices. If any of the search terms are ambiguous, a Resolve Ambiguous Terms dialog will appear. Open the options panel and confirm you are searching Homo sapiens with a Confidence cutoff of 0.40 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 263 up-regulated genes. To identify a relevant network, we will use the STRING database to find a network relevant to the list of up-regulated genes. With the filter active, select and copy all entries in the Gene Name column.But in this case, all genes with a fold change greater than 2 already meet that cutoff. Next, one would normally filter out non-significant changes by filtering on the p-value as well, for example setting p-value less than 0.05.In the drop-down for the fold change column, set a filter for fold change greater than 2.Select the row containing data value headers (row 4) and select Data → Filter.We are going to define a set of up-regulated genes from the full dataset by filtering for fold change and p-value. The file contains a summary at the top, and has 4 columns of data: Gene ID, Gene Name, fold change and p-value. Download the data: Transcriptomic analysis of autistic brain reveals convergent molecular pathology.The study has been published in Voineagu et al., and we will get a summarized dataset with fold change and p-value from the EBI Gene Expression Atlas. Cytoscape huge networks install#Install the Largest Subnetwork App from the Cytoscape App Store, or using the Cytoscape App Manager.įor this tutorial, we will use a dataset comparing transcriptomic differences between autistic and normal brain.Install the stringApp from the Cytoscape App Store, or using the Cytoscape App Manager. ![]()
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