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Upon joint inspection of the results of similarity searches of NR, GO and motif databases, EST contigs were assigned putative functions, and classified into broad functional categories, summarized in Table 1.
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Both house-keeping and tissue-specific functions are very broad functional categories and structural patterns in network organization have been observed.
Transmembrane proteins were grouped into broad functional categories based on domains known to be involved in specific biochemical functions.
Using bioinformatics, we putatively assigned contigs to broad functional categories and found that protein divergence was not evenly distributed among functional categories.
GO information was utilized to define the optimal number of clusters with respect to certain broad functional categories.
MG-RAST generated assignments of protein-coding nucleotide sequences to 29 broad functional categories of SEED subsystems and 637 narrow SEED subsystems (Level 1 and Level 3, respectively).
Based on the combined results of BLASTX and protein domain searches, transcripts were presumptively assigned to one of 23 broad functional categories (see Table 1).
c Broad functional categories are based on Gene Ontology [ 104] functional annotation by DAVID [ 105].
Percentage of orthologous genes and COG database genes distributed across the four broad functional categories.
The high tandem, low to moderate segmental duplication families fall into several broad functional categories.
We therefore analyzed the expression data in the context of broad functional categories.
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