What a long day! Tonight I continued watching the session on Exploring Plant Gene Linkages using Random Walk with Restart Tools. The apps were described and how the Random Walk with Restart tools can be used to explore networks. The output can be the top one hundred genes visualized in a network. The starting seed genes and others are ranked. The example given was a cellulose synthase gene and its connections in the network. Biological pathways related by network connectivity can be identified. A csv file can be saved with the most frequently explored genes by the network. Another app that was described is the feature set exploration in a multiplex network. The output visualization is similar with network connectivity. A ranks.tsv output from this app can be saved. The Functional Enrichment for GO Terms app can then be used to identify enrichments in gene ontology terms. The apps information links provide documentation and examples. Ben Allen facilitated the question and answer portion of the webinar. One question asked was what happens if you have a noisy dataset. The response addressed this by starting with the CV app to explore the connectivity and focus on genes with connections that you want to explore. Another question was about adapting the tools for yeast networks. I found this question intriguing: how tools can be used or adapted. However, it was noted that there the databases/data is not as rich as for bacterial, for example, data. This session was dense and provided some fascinating applications of new tools for network analyses.
