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The genomic locus of each candidate gene in the microarray was identified by aligning the EST with the Nipponbare reference sequence.
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409 probe sets (a technical term that describes a transcript on the microarray) were identified as differentially regulated between the BSE infected (n = 14) and negative (n = 12) samples.
3739 orthologues between the human FL microarray and the mouse U74Av2 microarray were identified based on curated Hu6800 orthology from Affymetrix [ 39].
A total of 583 (5.62%) of the 10,368 features from the cDNA microarray were identified as significantly different between aposymbiotic and symbiotic anemones (P < 0.01).
Hence, a total of 53 miRNAs, about 8.4% (53/632) of the probes on the microarray, were identified as putative differentially expressed miRNAs (P = 0.01) (Table 2).
In order to estimate the genomic representation of the microarray, Arabidopsis sequences similar to the citrus unigenes present in the microarray were identified and used for Gene Ontology [ 24] functional classification (see Material and Methods).
Using BLAST alignments of probe and cDNA sequences, the members of each isoform 'family' that could be targeted by either qRT-PCR or microarray were identified (typically multiple isoforms for each gene).
Besides focusing on ethylene, auxin and cell wall related genes, the 10 most up and down regulated genes in the microarray were identified together with their annotation and log2 ratio of expression between ACC treatment and control situation (Table 1).
To test whether LSGs in Arabidopsis thaliana display any distinct signature expression patterns, the expression patterns of 497 LSGs (with unique probesets on the affymetrix Ath1 microarray) were identified using the AtGenExpress developmental and stress series array datasets [ 59].
For data set #1, 12482 probe sets out of 54675 (comprising about 23%% of all probe sets on the microarray) were identified as potential markers associated with the five analyzed tissues.
In the miRNA microarray, miR-874 was identified to be upregulated by H2O2 stimulation.
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