The differentially expressed genes identified by transcriptomics and proteomics were assigned into functional classes based on a modified version of the Riley system [ 5, 35].
The gene families were assigned into functional categories based on the Clusters of Orthologous Groups of proteins (COG) database (Tatusov et al. 2000).
When seven was taken as the cutoff value, a total of 88 genes or possible operons, which could be assigned into nine functional categories, were picked out as the potential direct PhoP targets (see Additional file 10).
Next to the identification of processes related to different aspects of lipid catabolism, the "PPARα-tailored analysis" identified genes, mostly in vivo, that could be assigned into novel functional categories not previously linked to PPARα, such as "ECM", "cytoskeleton", "endothelial functions", "integrity of Golgi", "vesicular trafficking", and "endocytosis".
GO functional annotations were obtained using the Blast2GO program [ 123], and all unigenes were assigned into GO functional categories of molecular function, biological process, and cellular components using WEGO software [ 124].
To further characterize the functional features of those genes with antisense transcripts expressed in human hepatocytes, these genes were assigned into GO functional categories.
Subsequently, the 296 unigenes were assigned into 13 functional categories by a Gene Ontology assay.
In the analysis, the probe-sets on Barley Genome GeneChip were assigned into 35 major functional bins based on their molecular functionalities such as metabolic pathways, signaling pathways and gene families.
Although tremendous progress has been made through the application of such systematic studies, we found that within the S. meliloti proteome 3,376 (54%) proteins were not assigned to a functional category according to COGs, 290 (5%) have been assigned category S (function unknown), and a further 307 (5%) proteins have only been assigned into category 'R'generalral function prediction').
Putative functional kinases are assigned into one of the 55 Hanks and Hunter subfamilies (description in Table S6) using the following heuristic.
