We then generated mRNA expression profiles for these Pfam family members using Incyte's LifeExpress RNA (LE) database (Version 3.0, April 2001 release, Incyte Genomics, Inc .. We analyzed 135 Pfam families, whose family members are well represented on the Incyte microarrays.
Functional annotations were made by running PFAM (Punta et al. 2012) on the CLC Genomics Workbench v5.1 (CLC Bio Aarhus, Denmark), BlAST2GO (Conesa et al. 2005) and Reversed Position Specific (RPS -BLAST against the KOG-LE database (ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/, last accessed DecembeRPS -BLAST) with againstf of 1e−.
The LE database contains data points from a total of 976 probe pairs (Note: here the term of "probe" refers to "fluorescent-labeled total RNA sample used for microarray hybridization") that have been hybridized to one or more Human Genome chips 1~5.
Chat to any self-respecting French businessman and he will stare blankly when you talk of un ordinateur portatif, un agenda électronique, une banque de données or la marge brute d'auto-financement - he prefers le laptop, le PDA, la database and le cash-flow.
And Le Monde's Le Décodex, a database of more than 600 news sites that have been identified and tagged as "satire," "real," "fake," etc.
The BioModels Database (Le Novère et al., 2006b) also relies on it to provide PDF versions of its models.
In order to demonstrate the utility of our approach, we analyze the models of the 11th release of the BioModels database (Le Novére et al., 2006).
In Section 4, we use our approach to find inconsistencies in a large-scale analysis of the models of the BioModels Database (Le Novére et al., 2006) and compare our results with those obtained by other stoichiometric analysis techniques.
