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This could be explained by variation in structural features of the Health Records Department at the 4 sites as described above or in other organizational factors that we did not interrogate in this study, such as level of staffing and availability of resources.
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It is thus possible that the association seen with MM here may represent linkage to estrogen related effects, either through cross-regulation effects of the two genes or via linkage to another marker in the distal parts of ESR1 that does not show linkage to those markers we have already interrogated in this study.
A second major survival pathway interrogated in this study was PI3K, known to play a role in most cancers [24] [25], [42].
Although the SNPs interrogated in this study do not reach the level of genome-wide significance (p<5×10−8), our study nevertheless identifies 12 SNPs that replicate in two independent cohorts of MS cases and controls, and that reach a level of significance required for a candidate gene approach.
The database that describes human genomes and pathways, HumanCyc was interrogated in this study.
The QTL interrogated in this study are from previously published studies that mapped to the mm9 (NCBI build 37) mouse reference genome.
Relative gene expression in both UNC and TCGA sample sets was measured by normalized log2 ratios (Cy5 sample/controltrol) for each of the 70 genes interrogated in this study.
We find that 27% of all QTL interrogated in this study are covered by IBD bases, whereas 39% would be expected if they were randomly distributed.
Strains of E. coli and Shigella interrogated in this study consist of approximately 60 different serotypes and 75 isolates of the O157 H7 serotype (Table 1).
Our results therefore indicate that cell type-specific factors such as MITF contribute to the global organisation of the shared TFs interrogated in this study and likely play important roles in cell type-specific transcriptional control beyond the gene loci that are differentially bound by shared TFs.
Clinical and demographic data, PAM50 molecular subtypes, and GEO accession numbers for the UNC sample set are listed in Online Resource 1. Finally, Lowess normalized log2 ratios (Cy5 sample/controltrof) of the 70 genes interrogated for methylation in this study were median-centered prior to generating relative gene expression values.
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