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This improved the convergence of the genes between the datasets with 20 genes now consistently differently regulated across six of 13 datasets (data not shown).
Amongst the six TFs enriched in the SEREX-ovarian dataset, however, four, namely GATA1, MYOD, IK1 and HIF1, were also found in the Meta-UP dataset, indicating a weak link between the datasets with respect to transcriptional regulation.
Consistent with the general high correlation, most of the expressed genes varied moderately between the datasets, with a log2-fold change of 0.51 ± 0.47 (median ± s.d.; for the 6,947 genes expressed in both datasets with RPKM > 10 in at least one of them).
We chose not to include data collected in private hospitals for two main reasons: a) The data provided were frequently incomplete; b) It had previously been shown that inclusion of data from private hospitals had no impact on the ACSH rates (correlation coefficient of 0.938 between the datasets with and without private hospitals) [ 35].
There was no significant difference in observed heterozygosities (Ho) between the datasets with and without hybrids (Tables 4, 5).>> For some loci species-specific alleles were evident, e.g. in locus CM33 alleles 298 313 were common in Ch. parallelus but rare in Ch. montanus, while alleles 316 328 were common in Ch. montanus and rare in Ch. parallelus (Additional file 4).
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There is an overlap between the three datasets with 7 proteins supported by two data resources (Table 1).
Assuming that the results obtained from the datasets with the deepest sequencing depth were the most reliable results, we used these RDNPs as a standard to determine the level of consistency between the regions identified using datasets with lower sequencing depths and those identified using the standard dataset (Supplementary Fig. S8).
To allow better comparison between the datasets, each with a different number of social deficits, the social vulnerability index was also calculated as a proportion of the total number of deficit items by dividing the sum of deficit scores by the number of deficits considered (40 in the CSHA and 23 in the NPHS), yielding an index with a theoretical range of 0 1.
integrOmics also enables the inference of large-scale association networks between the two datasets with the use of network graphical displays (Fig. 1), where the edges represent relevant associations between the variables (nodes): Interactive graph drawing may be used to include more relationships in the network.
Excellent agreement was obtained between the two datasets with the small differences being attributable to differences in the spatial and temporal averaging inherent between the two datasets.
Next, the length variation patterns between the two datasets (with respect to the average domain size of a superfamily) were compared across each member and each superfamily for both database updates [Figure 4].
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