Cytoscape's software Core provides basic functionality to layout and query the network to visually integrate the network with expression profiles, phenotypes, and other molecular states and to link the network to databases of functional annotations. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. The IQuery result is automatically imported in Cytoscape and the resulting network, named Direct query result on network - HumanNet - XN (LLS >=3.5), contains known interactions between human query (prey) proteins, with a LLS score of 3.5 or greater.īefore merging our two networks, we should clear the Column Filterthat was applied previously.Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Click the Cytoscape icon in the top right portion of the screen to load the result in Cytoscape.We will use the result of querying HumanNet - XN, pre-filtered to contain only interactions with a LLS score of 3.5 or greater ("LLS" is a score specific to HumanNet). In the following results screen, select the Protein Interactions tab to view results from several public sources available in NDEx. Click the search icon to run your query.Paste the list of gene symbols into the iQuery text box.Open your browser and go to the NDEx website While confusing, the selection works correctly. Note: there is a minor issue with selection in which all of the columns are highlighted, not just the one that is selected.Click Ctrl+C ( Command+C if using a Mac) to copy.Now, select all the genes in the name column by selecting the top item, then scroll down and hold down Shift and then selecting the last entry.Then, use the Dropdown element to select the Uniprot column.Click the "Plus" sign and add a Column Filter.This interaction data will be obtained via the NDEx Integrated Query (IQuery) using the human prey proteins from our network.Ĭlick the Filter tab in the Control Panel Now extend the network by adding known protein-protein interactions between the human proteins. Click the Import button next to the AP-MS Demo Data network, then close the pop up window.Ĭytoscape will now display the interaction network with a default style and a grid layout (When loading from tabular data as described in Option 1, the layout may be different depending on your Cytoscape settings. The cyNDEx Browser window will pop up.Search the AP-MS Demo Data network in NDEx by typing "ap-ms demo data" in the NDEx Search Box and clicking the search icon. Option 2: Import the Interaction Network from NDEx For all other data values, designate them as Target Node Attribute, by clicking in the column header and selecting the red spreadsheet icon.Designate the AP-MS Score as an Edge Attribute.In the Import Network from Table dialog, select the Bait column as Source Node and Prey column as Target Node.Load the network via File → Import → Network from File., and select the Example data.Option 1:Create the Interaction Network from Tabular Data Use the App Manager to update all Apps to the latest version available.Latest CX Support App (v2.3.0 or higher).Note: You can also choose to skip the loading of the data to generate an interaction network, instead downloading a previously created network from NDEx. Note: This tutorial does not describe how to pre-process the raw AP-MS data, the data used here is already scored and filtered. In this quantitative AP-MS experiment, a relatively small number of HIV bait proteins are used to pull down a larger set of human prey proteins. The data used for this protocol is from an affinity purification-mass spectrometry experiment which identified interactions between human and HIV proteins by Jäger et al.
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