We used the TCGA dataset consisting of 209 Luminal A tumors as a discovery dataset (Table S1) and confirmed our findings in the other cohorts.
JAFFA also demonstrated excellent sensitivity and a very low false discovery rate on 250 bp reads simulating a MiSeq dataset (Table 2).
Initial phase information was calculated from a SAD dataset (Table 1).
Importantly, we found that LBFS values varied greatly between different statistical tests for a given dataset (Table 1).
Similar to the hStemModule, the hDiffModule was also positively correlated with ePSC_EB (NES = 2.793; FDR = 0) (Table 4); this observation was repeated with a separate dataset (Table 6).
The number of motifs identified within the narrow (P < =0.00164), broad with dominant peak (P < =0.00135) and broad without dominant peak (P < =0.00185) promoter datasets exceeded those identified in a randomized dataset (Table 4).
Furthermore, the intestinal identity of the C2.1 cluster is clearly shown by its very strong association (p = 2 × 10-26) to intestinal specific genes extracted from a public dataset (Table 3).
In KORA, 17 SNP-MET-LIP sets showed a causal relationship between MET and LIP (that is, MET → LIP) at the 5% significance level, however, none of them were replicated in TwinsUK at the same level of significance (although two of them were significant at 10% significance level and in need of further analysis in a larger dataset) (Table 2 and Additional file 1: Table S6).
To compare variance across experiments and transcripts, I first estimated the per transcript variance (σ2) across the mean log2 transcript accumulation per experimental unit for each transcribed locus measured within a given experimental dataset (Table S1).
By prioritizing VCF files containing 20 newly reported mutations in novel disease genes, we show that there is agreement between these results and those obtained from a larger, simulated dataset (Table 1 and Fig. 3), although the novel variant dataset prioritization was somewhat less accurate.
To verify an accumulation of proteins in a given ancestor term, we also compared the ratio of proteins annotated to a given GO term to the total number of proteins available from the GOA database, which was used as an unbiased standard dataset (Table S3 in additional file 5).
