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We first calculate the expression-based evidence E x (r) for all reactions to provide an overall ranking and to divide reactions into core and non-core sets.
The original confidence measures dividing interactions into a more reproducible "core" set and less reproducible "non-core" set [20] is coarse-grained and may often miss functionally informative interactions.
Non-core Set : genes that are found in at least one strain but not in all strains, and (iii).
In this regard, our Non-core set reflect genes that are found in at least one strain but not all strains, and HGT genes correspond to genes which are derived from putative recent horizontal gene transfer events.
Furthermore, only shotgun methods can interrogate the accessory genome, that is, the non-core set of genes that often differentiate pathogenic bacteria within a genus or species from closely related commensal strains.
The miRNAs are significantly enriched in the non-core TS set (P < 0.05).
A totally balanced TU game has a non-empty core set.
The sum of each row is interpreted as a measure of how authoritative all the non-core species are with respect to the new core set.
For the probe set-level analysis we used the full set of probe sets from the Exon Array including core and non-core probe sets.
In addition to the core probe sets, we extended our analysis to the non-core probe sets, which are those supported by EST and predictive evidence not present within RefSeq and full-length mRNA GenBank records.
This indicates that TF and miRNA are the major components of the non-core TS gene set.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com