Using this novel algorithm with stringent statistical criteria (FDR < 0.2) to a compendium of published and new microarray data (3, 6, 12, and 24 hr after Pou5f1 suppression) and published ChIP data, we identified 420 tentative target genes (TTGs) for Pou5f1.
Given the high rate of validation (based on RT-qPCR) of the in silico expression data obtained in a previous study based on the RNA-seq approach with stringent statistical criteria [ 32], we considered the data generated in this study to be accurate for the prediction of gene expression in vitro.
Analysis of the 45-MelCells microarray dataset with less stringent statistical criteria (Mann–Whitney test, p value <0.03 and difference in mean expression ≥1.5) allowed identification of a larger set of genes that were differentially expressed according to the CGAS.
Several of the most significantly differentially expressed genes were among those identified in the Baechler study (C1ORF29, MX1, LY6E, PLSCR1, and APOBEC3B) and others identified with less stringent statistical criteria were also found in the Baechler study (Table 2) or are closely related to genes identified by Baechler (OAS1, OAS2, MX2).
Other zinc transporters did not appear in the gene lists of significantly regulated transcripts, either because their expression was below the detection limits of the array or they did not pass the stringent statistical criteria associated with FDR associated with parallel analysis of >16 K genes.
We employed stringent statistical criteria, combined with a large sample size to support the identification of these VDAC1-covariant genes.
Using more stringent statistical criteria (t-tests p-value<0.05 with FDR correction, TNoM score = 0 and fold-change of expression >2, see "Materials and Methods" for details) we identified 103 genes whose expression significantly changed following ventilation in wild-type and/or in jnk1−/− mice.
We identified 11 of the 18 previously reported human ICRs covered by the Illumina Infinium HumanMethylation27 BeadChip panel, with additional ones which showed differences that were insufficient to reach our stringent statistical criteria.
We identified 451 genes overexpressed in lesional skin under more stringent statistical criteria (28 samples of lesional skin were matched with their non-lesional counterparts from the same patients in order to exclude individual expression variations, genes with fold change >2.5 and FDR-adjusted p-value < 0.01 were considered as upregulated).
Using stringent statistical criteria (see 'Methods'), we found that the genes regulated by osr mutants are largely overlapping with each other and with wild type ORGs (Figure 1B, Tables S2, S3, S4, S5, S6).
Using stringent statistical criteria, they identified two eQTLs in genomic regions that were also genetically associated with LDL cholesterol levels.
