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A final factor that complicates meaningful combinatorial analyses of transcriptional regulation is that integration of data from different studies and laboratories may be hampered by differences in experimental procedures for microarray experiments (including the use of different microarray platforms, mRNA extraction, normalization and summarization algorithms [ 3, 4]).
However, it is also important to note that the direct comparison of the findings from different groups can be complicated by differences in experimental conditions, for example the type of PFSPs used, which can be affected by many factors including the sonication conditions used for the preparations.
The discrepancy could be caused by differences in experimental approach, including the use of different mouse strains and different inoculation routes of tumor cells than those we employed in our present study.
These discrepancies may be caused by differences in experimental methods, tissue processing, or the use of different antibodies that recognize different epitopes.
Alternatively, this conflicting data could be explained by differences in experimental design.
However, for any single physiological parameter, significant variability exists among values reported by various sources; this discrepancy is often caused by differences in experimental methodology.
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By focusing on such direction of expression change measured by similarly behaving multiple genes, the analysis may become less affected by difference in experimental condition and assay platform.
This controversy in the reported data can be explained in part by an important variability in hypoxic response between the different species in these studies and by differences in the experimental models employed (acute versus chronic HPV, in vivo versus in vitro).
These potentially contradictory effects of IGFBP-5 in bone are further complicated by observations indicating that IGFBP-5 additionally may function in an IGF-independent way, and may have been accentuated by differences in both experimental design and methodology among published studies.
This could be explained by differences in the experimental conditions used; these authors studied the lipid raft association of SR-BI in membrane preparations from intestinal mucosa scrapings of fasted pigs.
Therefore, in order to minimize possible artifacts caused by differences in the experimental setup used in [7] and in this work, we also tested the leakage activity of CT 4 in the conditions similar to those described by Tjong et al. [7] (see Methods).
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