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RT PCR cases (n=69) included 15 cases profiled on microarrays but excluded from microarray analysis and 54 independent cases.
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Thus some of the transcripts identified in the LCM library may represent low abundance transcripts that would have been excluded from microarray analysis.
Missing values were not imputed, but excluded from analysis.
Unknown data are reported but excluded from further calculations.
Unidentified individuals were counted, but excluded from analyses.
CNS are also presented but excluded from relative analyses.
In order to confirm the results from the microarray experiments and to investigate the transcription of a few genes of special interest (excluded from the microarray results due to spot abnormalities), real-time quantitative RT-PCR (QPCR) was performed on 13 genes listed in Table 2.
Furthermore, the four genes which were excluded from the microarray results due to spot abnormalities (cpsC, ace, gelE and fsrB) were all found to be down-regulated in blood when examined by QPCR.
(HPaf and Suit007 had already been excluded after the migration assay. Capan-2 had to be excluded from further microarray analysis because of insufficient reproducibility).
DNA sequences corresponding to plasmids pAsa1, pAsa2 and pAsa3 were excluded from our microarray because they only had genes for self-existence, and no virulence factors [ 38].
Analysis using subjects excluded from the microarray analysis (Caucasian females) biologically validated the cotinine-dependent change in expression of two genes, CDKN1C and SASH1.
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