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Definition of company size was based on ranking by total revenues (Scrip's Pharmaceutical Company League Tables 2008).
Company size was defined as small, medium-sized, and large, based on ranking by total revenue as reported in Scrip's Pharmaceutical Company League Tables 2008 [ 13].
We give a formula based on ranking by P-values from a Wald test, but the current test of choice is the Cochran- Armitage test of trend, which is the score test from a logistic regression model [ Sasieni, 1997].
For all three interventions, the network signatures show a higher enrichment with known disease genes than the same number of genes selected based on ranking by differential expression, with 2.8 times higher enrichment for the DLI signature.
The network signature based on DLI showed significant enrichment for drug targets (p = 0.014), while the signature of the same size based on ranking by differential expression was not significantly enriched (p = 0.069).
Enrichment of genes known to be relevant to hepatic T2DM processes based on literature in the full network signatures (all genes that were assigned a positive score by the random walks algorithm), and signatures of the same size based on ranking by differential expression alone.
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Coherence of the constitutive transcription levels (or ND-induced transcription ratios) of various metabolic pathway-associated ESTs is defined as those whose relative occurrence density in one of the 3 half-ranges based on rank by level (or ratio) is 2-fold above background and p-value < 0.05.
Fourteen out of the 66 metabolic pathways exhibited high relative occurrence density in one of the 3 ranges of the pathway-associated ESTs based on ranks by level (i.e., 2-fold above background; p-value < 0.05), 5 of which were found to be enriched in the top 10% of the most abundant ESTs (i.e., 2-fold above background; p-value < 0.05).
We subsequently examined the relative occurrence density of the eRP- and aRP-encoding ESTs based on ranks by ratio between levels in ND and nitrogen-replete cells.
Relative occurrence density of individual metabolic pathways in ranges containing the first, middle, and second halves of the pathway-associated ESTs based on ranks by level was determined.
We also tested the occurrence density in the top 10% of the most abundant ESTs based on ranks by level or in the top (or bottom) 10% of the most upregulated (or downregulated) ESTs based on ranks by ratio (e.g., relative occurrence density >2-fold above background and p-value < 0.05) for coherently regulated metabolic pathways (see Methods).
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