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For poplar, microarray IDs corresponding to their orthologous FRK proteins were retrieved from the Plant Compliant Gene Expression Resources for Plants and Plant Pathogens (PLEXdb) website (http://www.plexdb.org/index.php).
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Corresponding microarray IDs for statistically significant probe sets were queried with an annotation database [ 23].
For reporting genes by name, IMAGE Clone IDs corresponding to the microarray probe sequences were used to extract UniGene Cluster IDs and names (Build 199 Homo sapiens; Jan 16 2007 [104].
Five types of IDs are supported: Ensembl IDs, Entrez Gene IDs, gene symbols and Illumina and Affymetrix microarray IDs.
Supplementary tables include gene IDs corresponding to both genomes nomenclatures.
Then, we obtained the rat UniGene IDs corresponding to Affymetrix IDs (15072 IDs).
Then, mouse UniGene IDs corresponding to Affymetrix IDs was obtained (this represents 14418 ID).
Then, human UniGene IDs corresponding to Affymetrix IDs for qualified genes were obtained using annotation file downloaded from the Affymetrix website (34097 ID).
The promoters were extracted for 323 Entrez IDs corresponding to the OC genes.
We then sorted the 513 genes by their unique Nimblegen microarray ID number (SEQID).
ID; RNA ID (this study); Type, RNA type; St., strand; Ov., overlap ; ID, RNA ID corresponding to the given reference; North., experimentally validated by Northern blot, given are the references for the Northern hybridizations.
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