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Each gene probe in each data set was mapped to a unigene cluster ID using the SOURCE database (source.stanford.edu).edu
Each probe in the data set was mapped to a gene symbol using the SOURCE database (source.stanford.edu).edu
First, gene annotation from each dataset was translated to UniGene Cluster IDs (Build #185) using the SOURCE database [ 26].
Clone annotation was updated using the SOURCE database [ 23], and the UCSC Genome Browser database and software tools [ 24] were used for clones without UniGene annotations.
Common elements between the data sets were found after translating the gene annotation from each data set to UniGene Cluster IDs using the SOURCE database [ 21].
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Relative expression of the EC-restricted genes in several normal tissues was obtained using the Source databases http://source.stanford.edu.edu
Gene annotations from each dataset were converted into UniGene Cluster IDs (UCIDs, Build 161) using the SOURCE database[ 43], and multiple occurrences of a UCID were collapsed by taking the median value for that ID within each experiment and platform, which resulted in ~2800 genes having expression data in all three datasets.
The Ingenuity Pathway Knowledge Base (IPKB) was used as the source database for biological function and pathway assignment to genes.
Probe remapping using the single source database, Ensembl, and the multiple source database, UCSC, were applied.
A further benefit of using the multiple source database, UCSC, is the ability to predict more alternative splicing events.
(A ) Three datasets were acquired in DDA mode and the peptides were identified using the open source database search engines (1% peptide-level FDR).
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