Exact(4)
The other two datasets display a similar trend.
However, do these independent datasets display the same covariation effects?
Besides, proteomics datasets display a systematic bias in function of abundant proteins, favoring "effector" proteins such as structural, inflammatory, core metabolism proteins but not the transiently expressed and fast degradable signaling proteins.
Considering all 19 inhibitors as well as both the REPTree and SVR regression methods, TSM datasets display the highest overall correlation coefficients (r) between actual and predicted relative susceptibility levels of the constituent HIV-1 PR and RT mutants (Additional file 3), a result similarly reported by the Stanford group (Table 6 in [ 24], available as online supporting information).
Similar(56)
Clustering of the NSI/SI and R5/X4 datasets displays a more pronounced grouping trend of the NSI and CCR5-tropic sequences than of the SI and CXCR4-tropic sequences.
IHAT successfully identified all fragments from each gene, with no false positives in the 1000 bp or 350 bp datasets, displaying a greater sensitivity to homologs than an expect-value cutoff of 10−35, used in previous similar studies [4], and similar sensitivity as a cutoff of 10−5.
The loading plots of all datasets displayed a similar influence of the genes to the first two PCs: the group of genes containing IL8, TREM1, SERPINE1, BIRC3, and TNFAIP3 were separated from the group containing VEGF, ADM, ZNF395, and KISS1R in the 2nd PC (Fig. 2A).
The obtained SEG measures were similar to those for the real datasets displaying stained nuclei.
Nevertheless, it is interesting how key molecules in two different datasets displayed predicted correlation patterns.
For datasets displaying non-normal distributions, non-parametric tests were also performed.
Fifty-seven genes activated in at least two of four tumor datasets displayed enrichment of cell-cycle components (Additional file 3).
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