In the case of genes essential using as a sole constraint to perform FBA the topology of a cancer metabolic network, there are two possible explanations.
All variants selected had a MAF < 0.003 for genes mainly associated with a recessive inheritance pattern and were absent from the databases in the case of genes associated with a dominant inheritance pattern (Supplementary Table S3).
In the case of genes essential when using also the exchange fluxes to perform FBA, but non essential when the sole topology was used as a constraint, an unfeasible solution is trivially attributable to the implementation of one (or more) of these additional constraints.
And unlike the case of genes, the argument that the alternative is quite different from what my imagined agent is currently doing is not necessarily a very good one: in the real world people do sometimes respond to opportunities by changing their behavior drastically.
That was what usually happened in the case of genes called linc-Foxf1a, linc-Hoxd3 and linc-Sox2.In two other cases, the embryos did come to term, but they were a lot smaller than they should have been.
Instead he discusses the special case of genes as replicators.
In the case of genes with multiple probes, the result for the probe with the greater signal intensity was chosen.
Similar behaviour was observed in the case of genes encoding Lpr, PsrA and GacA transcriptional regulators, that are likely positively affected by stringent response.
In silico analysis of CREs in promoter regions that included the first intron or exon (in the case of genes without an intron) of five genes in the Os1-CysPrxA group and six genes in the Os1-CysPrxB group revealed the presence of 40 CREs common to the promoter regions of both groups.
In the case of genes encoding proteins, that RNA produced from this process is messenger RNA (mRNA), which then needs to be translated by ribosomes to form a protein.
Tissue-specific expression levels were averaged in case of genes targeted by multiple probesets.
