In more detail, let Z be the vector of Z-scores for m SNPs functionally associated with the gene under investigation, Y be the diagonal matrix of the square root of imputation information for the m functional SNPs, S be the weight matrix, as derived from the SNP annotation database, for the m functional SNPs belonging to the k functional categories.
To determine whether genes down-regulated by miR-143 were related to specific cellular functions, we performed a search for enriched functional annotations as derived from KEGG and BioCarta pathway databases.
The set of annotations of a protein i as derived from GO is indicated by annotations(proti).
After this procedure, we re-collected all the pig proteome, and for each sequence, we collected the annotation as derived from statistically validated clusters, non-validated clusters and singletons.
Passport information is derived from annotation in the T. T. Chang Genetic Resources Centre database.
We here catalogue the R. culicivorax developmental toolkit derived from annotation of a draft genome sequence.
We evaluate clustering algorithms by judging how well the clusters correspond to groups of proteins as specified by MIPS complexes or functional modules as derived from either GO BP or GO CC annotations.
Annotation coverage refers to the percentage of protein coding genes holding a valid entry in the respective data sections for gene annotation, and at least one interaction to another gene as derived from interaction sources.
Homology-guided repeat annotation with a Triticeae-specific repeat library32 identified 3.7 Gb (80.8%) of the assembled sequence as derived from transposable elements (Table 1, Fig. 1a and Extended Data Table 3), most of which were present as truncated and degenerated copies, with only 10% of mobile elements intact and potentially active.
The GeneChip Human Exon 1.0 ST array was designed to be as inclusive as possible at the exon level, deriving from annotations ranging from empirically determined, highly curated mRNA sequences to ab-initio computational predictions [ 11].
An analysis of the DE transcripts was performed using only the top DE transcripts with annotation derived from primary annotation sources rather than passaged secondary annotations (Table 3).
