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Gene Ontology (GO) Biological Process classifications were assigned to 144 (77%) of the DEG.
COG classifications were assigned to each protein by comparison to the COG database [ 28].
Functional classifications were assigned to reads according to the COG terms.
To achieve a functional annotation of the infection-responsive genes, GO classifications were assigned to the 1996 differentially expressed genes by using DAVID (Additional file 5, Table S5).
Where possible, Gene Ontology (GO) classifications were assigned to each protein translation based on BLASTX (E-value<10-5) similarity to entries in a GO-annotated database (UNIPROT).
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Only 25% of those with the "bad" classification were randomized to Arm B while 62% of those with the "good" classification were assigned to Arm B and so in this small study, the treatment arm assignment might confound the assessment of the serum proteomic classifier and vice-versa.
PAM50 subtypes (including the CL classification) were assigned to each sample using previously published methodology [ 36, 55– 55].
(4) Taxonomic assignment: a taxonomic classification is assigned to each sequence of the representative set with the GreenGenes database and newly defined taxonomies from step 2. (5) OTU table generation: an OTU table is constructed in the Genomics Standards Consortium candidate standard Biological Observation Matrix (BIOM) format.
Another advantage of this approach is that the index ensures that a certain number of basic indicators are assessed clearly before an overall classification is assigned to a given water body.
In addition, the contribution of each gene to the correct classification was assigned to each donor.
Classification was assigned to the category with the largest output value.
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