As expected, gene set enrichment analysis (GSEA) confirmed that the organoid cultures are enriched in genes specifically expressed in adult Sox9+ pancreatic duct cells.
We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae, (2) reconstruction of gene arrangements ancestral to A. gossypii, S. cerevisiae, and K. waltii, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets.
Four lines of evidence are used here to test if DS patterns are necessary and sufficient conditions for the occurrence of WGD in yeast: (1) pairwise comparison of gene arrangements, (2) reconstruction of ancestral gene arrangements, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets.
Although such comparisons rely on many assumptions and may in addition suffer from a somewhat uncertain definition of the set of expected gene models, the losses of genes in G. salaris, as well as in tapeworms and flukes, appeared much higher than in other bilaterian lineages.
We then extrapolated the expected gene density per deletion bin to the whole set of chromosome 3B genes.
As expected, these gene sets are smaller than the corresponding set with duplication in A. oryzae.
Although such topics are expected for gene sets with genetic association, it is the functional aspects of the gene sets related to the diseases that are more interesting.
Intuitively, we expect ORB+ gene sets to have suffered more structural (and perhaps functional) disruption in the course of LGT than have the ORB− sets.
As one would expect, several gene sets were also identified that are involved in the cellular response to GCs or other drugs.
The module expects that gene sets S consisting of gene identifiers and associated classifiers, and gene list L consisting of unique gene identifiers and associated P values from a study of interest.
