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To evaluate the contributions of the individual feature types of the input vectors, we used a representative gene set of the A.thaliana experiments for illustration.
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The aim of this paper is to discuss and compare these different modelling approaches, using a representative gene regulatory network.
Second, we performed the Fisher's exact test (which does not depend on the normal distribution of data) using a representative gene as a reference.
We used a representative example of SIRT2.
To search the database, an Affymetrix GeneChip ID or a representative gene ID is used to 'Search by IDs' or a paste sequence is used to 'Search with BLAST' [ 44]; two or more representative gene IDs are used to 'Retrieve PCC with gene list'.
Lastly, in a separate analysis we created phylogenetic profiles for each putative cow tRNA gene using a representative set of genomes to gain an overview of common evolutionary histories of tRNA genes.
We reanalyzed the phylogeny of CAD and CAD-like genes using a representative dataset including lycophyte and bryophyte sequences.
CEGMA uses a representative set of 458 Core Eukaryotic Genes (CEGs) that are highly conserved between eukaryotic species.
As with our mitochondrial analysis, to reduce the impact of the node density effect in maximum likelihood substitution rate estimates we used a single representative nuclear gene sequence for each clade.
The Roche Nimblegen Whole Human Genome Expression profile microarray was used to detected representative gene expression profiles of hDPSCs by ginsenoside Rg1.
We consequently used cel6a/cbh2 as representative gene for evaluation of genes coregulated with cellobiohydrolases in the presence or absence of BLR1, BLR2 or ENV1 as described above in light and darkness (Additional file 2: Table S2).
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