Ideas for more analysis

Question

[The Last Word]

Hi all,

I have a network that I split into 8 clusters using a clustering algorithm. I further calculated the hub genes and the network parameters of these clusters.I further used DAVID to go a Gene Ontology analysis of these 8 clusters.

I found the orthogonal genes in Drosophila of the genes in each cluster and using GENEMANIA created 8 corresponding clusters for Drosophila. I found the hub genes in these 8 clusters and did a Gene Ontology analysis as well. My main aim was to compare and see if the genes were part of the same gene ontology functions in both Drosophila and the first species that I had.

I am however now stuck as to what more I can do with these networks. Most papers I read finish off their research with GO analysis. What more do you suggest that I could do with my clusters. Any ideas are welcome. I have all the clusters on Cytoscape, so I can use the vast resources available on cytoscape for my work.

[Sean Davis]

What biological question are you trying to answer?

[The Last Word]

@Sean Davis That is what I was wondering myself. Other than compare GO terms to check biological similarity or dissimilarity, is there any other biological question I could investigate through a comparison of the gene networks of two orthologous species.

Answer 1

[xanderpico]

There are indeed many directions you could go within Cytoscape. As mentioned before, much of this depends on what your biological question is, as well as what data you have. Key information is missing for me to give you a specific answer, e.g., how did you get the original network that you then clustered and annotated? You "found the orthogonal gene in Dm"... what was your original species? Why would you want to compare the GO annotations between two sets of orthogonal genes? Are you investigating the quality of GO annotations? Do you have a hypothesis for why orthogonal genes in Dm perform different biological processes? Etc...

Finding the right questions is a key part of an exploratory analysis. Here are some resources that might help:

• A paper on "Finding the Right Questions": http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000472
• Browsing the Cytoscape app store by category:
  
  • Enrichment Analysis: http://apps.cytoscape.org/apps/with_tag/enrichmentanalysis
    • e.g., this collection of apps: http://apps.cytoscape.org/apps/functionalenrichmentcollection
  • Network Alignment/Comparison: http://apps.cytoscape.org/apps/with_tag/networkcomparison
• Browsing prior work using Cytoscape: https://cytoscape-publications.tumblr.com/

Hope this helps!