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The randomized database was tested for the presence of the aforementioned patterns and randomization and testing was repeated 100 times.
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Enrichment was tested for the functional categories derived from the gene ontology database [ 38], the COG database [ 39], the Protein Information Resource database [ 40], and the InterPro database [ 41].
Despite the fact that the database has been tested for data-safety of insertion from multi-centric data-management [ 12], in this study section all data were inserted by a single data-manager.
Of the 360 patients in the database, 294 had been tested for AFP.
Of the 250 compounds in the database, 220 have been tested for their binding affinity to human TTR.
But most of the nearly 6 million SNPs in public databases haven't been tested for in multiple people.
Each SNP was mapped to the closest gene within 1 Mb; 88 of 91 and 103 of 108 genes were present in the PANTHER database, and these subsets were tested for correlation with 241 biological processes and 176 pathways classified in the database (32).
Both C2 (canonical pathways and signatures from the literature) and C5 (gene ontology terms) gene set collections from the MSigDB database (http://www.broadinstitute.org/gsea/msigdb) were tested for enrichment and gene sets with FDR < 1% were considered significantly enriched.
Pathways obtained from MSigDB (database of gene sets provided by GSEA) were tested for enrichment.
The stoichiometric consistency of the universal reaction database and of the metabolic reconstruction can be tested for permitting the computation of biologically more relevant solutions.
These procedures exploit the fact that the probes designed for a primary species (i.e. generally perfectly matching to primary species transcripts) can be tested for matching to database transcripts of a secondary, interrogating species.
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CEO of Professional Science Editing for Scientists @ prosciediting.com