For smoking cessation, there are various suggested protocols and the 5-points National Acupuncture Detoxification Association NADAA) protocol is the most widely adopted one (5 annotated arrows in Figure 1).
We have assessed the quality of the predicted modules that contain the known CESA genes responsible for secondary wall cellulose, namely CESA4, CESA7 and CESA8, which have been widely studied and well annotated [ 12, 13, 23].
Thus, differences in the complement of genes carried by an E. coli strain are not due primarily to duplication of long-established genes that are widely distributed and well annotated, but are overwhelmingly due to gain of genes that are poorly known.
The source code and documentation are publicly available for download from The identification of conserved DNA sequences by comparative genome sequence analysis has been widely used to annotate both protein-coding and gene regulatory elements in a wide variety of taxa [ 1- 5].
Within the open biomedical ontologies (OBO) umbrella, gene ontology (GO) is widely used for annotating genome sequences and their functions, and parallel efforts exist in anatomy [16].
Most useful was the Gene Ontology [67] which has been widely adopted to annotate and classify large scale results and can be used for searching and classification in the MPD.
Specifically, we use: The Gene Ontology (GO) [22], which has been widely used for annotating function and localization of genes at a coarse level in many organisms [23], [24], [25], [26], [27], and The pathways that regulate and execute the processes that one is interested in studying, as defined in KEGG [28] (one can also use MetaCYC [29]).
Among them, GO terms have been widely used to annotate the functions of gene products [ 3, 8, 9].
In fact, gene expression data has been widely exploited to annotate protein functions (guilt by association) and predict novel protein-protein interactions [ 50- 52].
