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Although searches against the NCBI non-redundant protein and nucleotide databases produced matches for a further 5,909 contigs, these were excluded from the annotated transcriptome as few had available functional annotation.
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Additional tabs contain raw lipidomics results (including the abundance of several sphingolipid species with odd numbered fatty acid chain lengths excluded from the analysis), annotated therein.
The genes that were excluded from the RefList were sparsely annotated (36% GO annotation; 3% KEGG annotation), consequently the loss of information due to excluding these genes was negligible.
TN (true negatives) are the proteins excluded from the clusters that are not annotated to the term.
We separately annotated and excluded from the transposable element counts elements that could not be categorized and elements without typical transposable element features that contained profiles from protein coding genes.
Another evaluation set was composed of organisms that were initially excluded from the analysis, as NCBI Genome Project does not annotate them as either pathogenic or non-pathogenic.
Exons and introns were defined according to the canonical splice isoforms; annotated UTRs were excluded from the analyses.
PTEs that might correspond to 3′ or 5′ splice sites (SS) of not annotated exons were also excluded from the analysis.
The proteins which are only annotated with GO term inferred from electronic annotations are excluded from the experimental datasets.
Entries annotated as being genomic sequences were excluded from the analysis.
Genes that were not annotated or not easily classified were excluded from the functional clustering analysis.
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