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There was concordance in expression for these differentially expressed genes in monocytes and PBMC samples.
There was also concordance in expression between primary tumors and bone marrow.
The concordance in expression profiles in autopsy tissue was also investigated by pair-wise comparisons of all cardiac expressed genes, expressed as the fold change between time-points,.
Finally, we assessed whether there was any concordance in expression of eIF2α, phospho-eIF2α, and BiP in any tumor cell compartment.
Concordance in expression of the two antigens was seen in 71% of SCLC samples, with 35% expressing both antigens strongly, 8% moderately and 28% being negative for both antigens.
The baseline explant and autopsy and their later timepoints, showed similar concordance in expression and we saw no difference from technical replicates (95.9% and 93.4% genes with ≤1.25 fold change, respectively) (purple and brown lines, Figure 6).
Similar(53)
Just as in the case of the protein coding genes, the high-concordance in expression patterns of these categories of ncRNAs, suggest that these transcripts reflect marshaled events.
Analysis of the relative mRNA levels for the top 10 up and down regulated genes (see Suppl Table S1) by qRT-PCR confirmed the differential expression of all these genes (Fig 5), and showed an overall concordance in relative expression levels with that obtained from microarray analysis.
The Spearman correlation for mean expression in overlapping genes across the two data sets was 0.81, demonstrating good concordance in overall expression levels between the data sets despite substantial differences in sample preparation and health status (the participant in the Snyderome study suffered from type-II diabetes during part of the study).
Given the high overall concordance in gene expression profiles found among the three donors in our analysis, the fold change of gene expression levels in response to either H5N1 or H1N1 compared to mock infection was averaged from the three donors in the subsequent analysis.
We have previously described age-related gene expression changes in human stem and progenitor cells and observed a moderate but significant concordance in the expression profiles upon aging in vivo and replicative senescence in vitro (Wagner et al., 2009).
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