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Single population analysis according to Gene Ontology (GO) annotation revealed remarkable variation among batches.
In single population analysis, overrepresentation of polycomb target genes was found among the lists of SYT-SSX1-induced genes in all four hMSC populations.
Both lists derived from the analysis of the four hMSC population together and lists derived from single population analysis were used, (table S7).
Single population analysis revealed hMSC isolate-specific transcriptional changes involving genes that are important for biological functions of stem cells as well as genes that are considered to be molecular markers of synovial sarcoma including IGF2, EPHRINS, and BCL2.
Similarly, single population analysis revealed greater similarity of some MSCSYT-SSX1 population transcriptomes than others to SS gene expression signatures, supporting the hypothesis that features which distinguish independent hMSC isolates and contribute to their heterogeneity may be key for SYT-SSX function.
Consistent with the variability of MSCSYT-SSX1 transcriptome relatedness to SS signatures and that of GO term overrepresentation, single population analysis limited to datasets of epigenetically regulated genes showed marked qualitative and quantitative differences among the four hMSC isolates, the most striking being the divergent effect of SYT-SSX on the expression of imprinted genes.
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The results obtained by using multi-populations overlap with the single-population analysis (Figure 4).
Nevertheless, it is important to perform further extension of the study to gain better statistical power to investigate this association in a single-population analysis and further to replicate the association in independent cohorts of Asian origin.
Joint linkage analysis, using multiple segregating populations, could overcome some of the inherent limitations associated with single population linkage analysis and genome-wide association mapping [ 8].
Considering the peninsula as a single population, the analysis unsurprisingly finds that the highest mean proportion of ancestry corresponds to the Basque parental population.
In the single population linkage analysis, this QTL CI with significant additive effects was only significant in population D. In the greenhouse experiment, we observed significant QTL with significant additive effects for EX and IR which colocalized with the QTL on chromosome 10 identified in the field experiment in the connected analysis.
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