To begin, open a web browser and navigate to the link to access the Joint Pathway Analysis functionality on the MetaboAnalyst website. Access the folder where the output files from implementing DeepOmicsAE are saved, and open the text files named module_n. txt for each signaling module generated.
From the text files, locate the list of proteins and copy them. On the MetaboAnalyst webpage, paste the copied list of proteins into the gene's proteins with optional fold changes window. Repeat for metabolites, pasting them into the compound list with optional fold changes window on the same webpage.
Choose the relevant organism and the ID type. Then, submit the information by clicking Submit at the bottom of the page. On the following page, verify the ID mapping to ensure that the identifiers are correctly recognized, and then click Proceed.
In the Parameter Setting page, select Metabolic pathways integrated or All pathways integrated to visualize the contribution of input to metabolic or all signaling pathways. In the Algorithm Selection panel, choose Enrichment analysis, Hypergeometric Test;Topology measure, Degree Centrality;and Integration method, Combine p values pathway-level. Click on Submit at the bottom of the page.
The final page, Result View, will display the outcomes of the enrichment analysis. This includes plots of enriched pathways based on their impact and significance and a tabular list of pathways. MetaboAnalyst interpretation of the signaling modules obtained upon DeepOmicsAE on a dataset from brain samples of healthy or Alzheimer's patients revealed that for each signaling module, distinct metabolic and signaling pathways were enriched.
Moreover, the characterization of interactions occurring between clinical features and signaling modules showed that the altered glycerolipid metabolism in the Alzheimer's patients was associated with their sex and age at death. Conversely, alterations of synapses and axon functionality tend to occur across Alzheimer's patients, irrespective of their sex, education level, and longevity.
