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These scores are much higher than the score obtained by using all the genes.
However, coexpression networks can be built using all the genes on the microarray chip.
GO profile comparison was done using all the genes under sDp2 and all the essential genes as identified by RNAi collected from WormBase WS230.
It should be noted that the aforementioned co-expression network analysis was performed using all the genes with and without known functions.
I would limit the use of new terms to when they are absolutely required Authors' response: Wild genome forest is only the name of one of the two forests we studied, reconstructed using all the genes from E. coli UTI89 (NC007946) as indicated in M&M.
Principal components analysis was computed with R's prcomp function using all the genes present on the microarrays.
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To perform statistical analyses of the different groups we used all the genes from each group.
However, for Refseq-rheMac3, we used all the genes because of its conservation in annotations.
First, network-based analysis can use all the genes, whereas pathway-based analysis uses only annotated genes.
It is noteworthy that we used all the genes to calculate the correlations without filtering out genes that are not differentially expressed or not detectable across the three tissues.
On the same subset, ContrastLow ranking method that used all the gene scores but GAGE2A resulted in 74% overall accuracy (Matthews correlation 0.55 and AUC 0.62).
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