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In contrast, our approach is fully automated and handles multiple functional annotations per gene.
Prioritisation is based upon the assessment of patterns of multiple functional annotations.
Due to the high redundancy that exists between pathway databases coming from multiple functional annotations of gene products, pathway enrichment often results in a long list of potentially interesting pathways.
As a summary metric, the accuracy of a prediction, Acc, can then be defined as the geometric average of sensitivity and positive predictive value, (8) As we gained more and more biological knowledge about the proteins, we can associate a protein with (possibly multiple) functional annotations.
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We have developed a system that combines a unique collection of data from multiple functional annotation categories to prioritise variants by predicted function.
Even though the complexity of the transcriptome cannot yet be fully appreciated, we developed a tool to easily and promptly obtain information from multiple functional annotation systems (Gene Ontology, MapMan bin codes, MIPS Functional Categories, PlantCyc pathway reactions and TAIR gene families).
Conversely, for lower scores, the subnetworks included broad networks with multiple, non-specific functional annotations.
We then used these gene and enhancer clusters as the foundation of our functional downstream analyses that integrate multiple sources of functional annotations and molecular data.
Because some of these unigenes were annotated with multiple COG functions, altogether 15,701 functional annotations were produced.
As some of these sequences were annotated with multiple COG functions, altogether 29,337 functional annotations were generated.
Since some transcripts could be assigned multiple KOG functions, altogether 46,291 functional annotations were produced and all hit transcripts were grouped in 25 categories (Tables 3 and 5).
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