This discrepancy was mainly due to differences in the stringency of the data-processing algorithm.
We observed that typically over 90%% of genes called differently expressed with microarray, even with a low stringency screen of the data (FC > 1.5), were independently confirmed with RNA-seq.
In total, 45 genes were identified as significantly changed, using a relatively low stringency screen of the data, with a p-value cutoff of <0.05, and fold change >2 (Table 3).
Our screening pipeline to search for putative opsin candidates included three different filtering stringencies of the raw data (Filter15, Filter25, Filter30), two different assemblers (CLC, IDBA), and two different search algorithms (BLAST, HMMER) (see the Materials and Methods section for more details).
Therefore, the stringency of activity data and compound selection decreased from the high-confidence set over low-confidence set 1 to low-confidence set 2. Progression of drug promiscuity over time was systematically evaluated on the basis of all three data sets.
Regardless of the method and stringency of data filtering performed, the average expression of Z-linked contigs between males and females was essentially identical, suggesting the complete compensation of Z-linked genes.
This is fewer than expected in comparison to previous reports on differential regulation during spontaneous Caco-2 differentiation and probably due to the difference in stringency of the algorithms used for data analyses (MAS 4.0 vs RMA), rather than related to functional biological discrepancies.
Thus, strong and validated disease signatures depend on the stringency of data analysis and comparison with apparently unrelated, publicly available data sets from other studies.
When the stringency of data selection criteria was gradually relaxed and low-confidence data were considered, unrealistic increases in promiscuity over time were detected.
A relatively low stringency screen of the microarray data (P < 0.05, FC > 1.5) comparing wild type and mutant podocytes identified 73 annotated genes with higher expression in mutant podoctyes (Additional file 7: Table S7).
