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The sophisticated analysis tools of YGA can identify distinct biological features between two gene sets, which help biologists to form new hypotheses about the underlying biological mechanisms responsible for the observed difference between these two gene sets.
We found that there were few overlaps between two gene sets; no overlap in top 20 genes, and only two overlaps in 200 genes.
Size of a node varies by gene set size and the thickness of the edge represents the degree of correlation between two gene sets.
Angular distance between two gene sets is determined from Δ and is proportional to the similarity of the gene sets' enrichment profiles.
In a gene set network (GSN), a node represents a gene set and an edge represents a relationship between two gene sets.
A past study proposed a method to measure a functional relationship between two gene sets based on protein interaction network [ 35].
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We identified modestly significant (unadjusted P value < 1 × 10-4) overlaps between three gene sets in this subnetwork with two gene sets related to cell cycle (NRC-1 and NRC-5) and one related to cell growth (NRC-9).
We noticed the difference of sample sizes between HK and TS genes when comparing correlation coefficients between such two gene sets.
Two sets of genes were randomly generated from all genes in the whole Drosophila genome and the proportion of overlapping genes between the two gene sets was calculated.
Visual examination of Figure 6 indicates that the linkage between these two gene sets is driven by the genes F2, Plg, CYP2E1, Nr1h4, Lipc, and their interactors, with weaker contributions arising from Hnf1a and Hnf4a.
For GO Cellular Component, six terms were the same between the two gene sets.
More suggestions(16)
between two gene products
between two gene models
between two rank sets
between two gene variants
between two point sets
between two gene profiles
between two gene phylogenies
between two gene networks
between two gene families
between two gene sequences
between two gene lists
between two gene orders
between two gene nodes
between two gene neighbors
between two gene carts
between two gene pools
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