If specific guidelines are not available, assignment of drug response phenotype is based on observations from published clinical outcomes data for the specific drug-gene pair.
Two strategies were applied for gene expression signature analysis: (1) When centroids for specific classes (e.g. BC subtypes or groups of ER-negative breast tumours [ 25]) were publicly available, assignment of BC cell lines to these classes was based on their highest Spearman rank correlation.
In order to produce a preliminary hypothesis on this question, each gene was assigned to a single biological-process GO category, chosen among the available GO assignments (see methods), with genes assigned to multiple GO categories assigned to the single GO category containing closest-to-125 ENCODE [ 28] genes.
We have compared the assignment of the three available PPII assignment methods and specifically analyzed the distribution of PPII based on these assignments.
Some graphical methods have been proposed for designing such experiments, however, all these graphical methods need linear graphs or interaction graphs available for assignments and all have their limitations.
Also, the therapists would highly appreciate a large database of available online assignments.
For avoidance of bias, all available writing assignments were analyzed and included in the final assessment.
When structural data were available, our assignments were in good agreement with the literature.
Later when the genome sequences of the pathogen and host became available, the assignments were checked and if necessary corrected.
