To begin, download a sample comma delimited input file containing metabolite measurements. Double click on the downloaded sample file to open it and ensure it contains sample names in column one and group assignations in column two. The remaining columns contain metabolites and each row represents a sample.
Next, download the Filigree Java application and double click on the downloaded. jar file to launch the application. On the Data tab, click the Browse button to upload the input file.
Under Specify Columns or Rows, click the dropdown arrow next to sample ID to select the corresponding column or row name from the input file. Then select Sample. Next, click on the dropdown arrow next to Group to select the corresponding column or row from the input file and select Group.
Under Specify Sample Groups, click the dropdown arrows next to each group to select the corresponding group column from the input file. Under Feature Grouping, check the box next to the desired method, calculate feature groups. Click the view heat maps to view the heat map and determine a desired percent reduction.
Next, using the feature reduction slider, select the desired percent reduction of features and slide the small circle until the percent reduction shows a feature-to-sample ratio of 1.25. Click the next button to move to the Analysis tab. Under select output directory, click the browse button and select the desired directory location for storing the generated output files.
Click on the Run Analysis button. Upon displaying the message, analysis completed successfully, click the Okay button on the popup window. Next, on the Analysis tab, click the Browse Networks button to open the interactive filigree subnetworks in a browser tab.
Under the subnetwork name column, click on the Subnetwork 1 link. Then explore the interactive subnetwork by clicking the plus button and zoom in on the part of the network and click the minus button to zoom out. Click on a group node and drag it to reposition it within the subnetwork.
Then click the Expand Features button to expand all the group nodes and review the specific compounds that make up the group nodes. Then click the Collapse Features button to collapse the recently expanded group nodes. Next, click the By Sample Group button to change the view from a single subnetwork to multiple subnetworks split by a group.
Then using the view of the subnetworks, explore and compare the groups. Click the All Samples button to go back to the single subnetwork view and click the Next button to view the next subnetwork. The differential network constructed using the plasma metabolite measurements from Type 1 diabetes and non-diabetic mice revealed a higher degree of network connectivity in the non-diabetic group.
Enrichment analysis results showed that nine of the 12 metabolic modules identified were significantly different between Type 1 diabetes and non-diabetic mice.
