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Such classifications are done, however, to systematically categorize the numerous known poisons.
These hierarchical classifications are performed with results of each DE analysis (with a type I error equal to 5%) by setting to 1 the genes that are upregulated, to −1 those who are downregulated and to 0 those who are not significantly DE. (Hierarchical classifications are done with the R function hclust with Euclidean distance matrices and argument method = "complete").
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Classifications were done with SNID (Blondin & Tonry, 2007, ApJ, 666, 1024) and GELATO (Harutyunyan et al., 2008, A&A, 488, 383).
The PLS classifications were done using a PLS regression implemented using the kernel algorithm available in the PLS [57] package in R [55].
All classifications were done manually.
All classifications were done using the same set of features.
Pathway classifications were done manually using the Pseudomonas genomic database (pseudomonas.org) and the KEGG Pathway module.
All radiographic measurements and classifications were done by VK, who was blind regarding all background information, including drug treatment.
For the first one hundred articles, the classifications were done independently followed by a consensus discussion in the event of discrepant classification.
Most classifications were done at the time when patients visited the clinic, and only a few were classified retrospectively based on the patient chart.
Protein localization and functional classifications were done using PSORTb [ 77], InterProScan [ 100], Conserved domains and CDD domain architecture-Search tool on NCBI [ 101].
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