To determine a subset of genes common to the three platforms, we used the mapping provided by the MAQC study [ 14] to select 12091 probesets common Illumina and Affymetrix U133 arrays.
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The probe sets for the remaining arrays were subsequently mapped to Ensembl transcripts using the mappings provided by BioMart.
The UMLS IDs were converted once more into ICD-10-CM (International Classification of Diseases, 10th Revision, Clinical Modification) using the mapping information provided in the UMLS.
Mouse and rat genes were mapped to their human orthologs using the mapping files provided by MGD (ftp://ftp.informatics.jax.org/pub/reports/HOM_MouseHumanSequence.rpt) and RGD (ftp://rgd.mcw.edu/pub/data_release/RGD_ORTHOLOGS.txt), respectively.
Features on the array were mapped to Entrez Gene [16] IDs using Version 9 of the mapping provided by Dai and colleagues [17].
Briefly, raw microarray data was collected from NCBI's Gene Expression Omnibus (GEO) [25], [26], and features on the array were mapped to NCBI Entrez Gene IDs using Version 9 of the mapping provided by Dai et al. [27], yielding 16,297 gene probe sets and 64 Affymetrix control gene probe sets.
We also searched protein sequences against the Pfam library of hidden Markov models (HMMs) [ 98] using HMMER, and mapped Gene Ontology (GO) terms to Pfam entries using the 'pfam2go' mapping provided by the GO consortium [ 99].
In order to score conserved domains, SCOP structures that were scored as "CERTS" were mapped to Pfam domains using the PDBMAP mapping provided by Pfam.
The complete set of available reads was realigned to contigs using the mapping assembly method provided by the Roche GS Reference Mapper, specifically designed for consensus alignment of reads against a given reference sequence.
