To further characterize the CRC subtypes at a functional level, we subjected the lists of subtype signature genes to a functional analysis using Signaling Pathway Enrichment using Experimental Datasets (SPEED) [ 45], the Molecular Signatures Database (MSigDB) [ 46], and KEGG [ 39] and Pathway Interaction Database (PID) [ 47] using BioMyn [ 48].
During the past years, the subtype nomenclature has been undergoing many revisions: for instance, subtypes E and I have been discovered to be indeed recombinant forms and removed from list of pure subtypes.
When we compared the list of specific subtype miRNAs with that of the miRNAs influenced by DNA copy number changes we found 15 miRNAs shared between the two groups, representing a statistically significant overlap (Fisher test p-value < 0.001).
Studies with ligands such as GABA and general anaesthetics have further confirmed and extended the list of GABAA channel subtypes [ 16].
Predicted secondary structures for subtype-specific ESS3 stem loop structures, one-dimensional H NMR spectra for each cytosine-substituted construct, and a complete list of group M subtypes aligned for phylogenetic comparisons (Table S1).
The list of GABA-A channel subtypes has been further extended and confirmed with other ligands such as GABA and the general anesthetics (Olsen and Sieghart 2009).
(For a complete list of peaks by enriched subtype, see Table S4).
We can now add Luminal A disease to the list of heterogeneous diseases with distinct subtypes within this previously defined single subtype.
Because the frequencies of p53 status varied significantly by subtype, the list of p53-associated genes defined by SAM includes genes that were associated with subtype.
Finally, by comparing the three related but dissimilar cell lines, we are able to refine the list of markers that distinguish between different subtypes of endoderm including those that distinguish DE from VE. Endoderm both embryonic and extra-embryonic has been shown in various model systems to play an inductive role in the differentiation of mesodermal and ectodermal tissues that adjoin it.
