Our primary hypothesis regarding this dataset was that should hsa-miR-124 selectively down-regulate target transcripts via a seed-pairing directed mechanism then the nucleotide complement of the hsa-miR-124 seed sequence should be preferentially enriched in the down-regulated transcript population.
We believe that these results can be further improved by incorporating the available important details regarding the dataset under study.
For this example, a random sample of four anonymized patients was extracted from the QIDS data imputed using last value carried forward (see "Secondary analyses" for details regarding this dataset).
Further details regarding the dataset can be found in Table 1.
The PLS2-DA model was chosen as there were constraints regarding the dataset: qualitative variables, multicollinearity issue and not applicable data.
Regarding the dataset of sensitive mutants, the most enriched terms were "mitochondrial translation" and "translation", evidencing the importance of protein synthesis in coping with both stresses.
Specifically, the method only used expression values while expression databases also provide textual information both regarding the dataset (an abstract) and regarding the individual arrays (time point, exact condition, etc).
We are thankful to Sassan Saatchi, Sangram Ganguly, Barry Tyler Wilson, Rachael Riemann and Josef Kellndorfer for providing their datasets and clarifying questions regarding the datasets.
See Supplementary Appendix 1 and Supplementary Table S3 for more details regarding the datasets.
Although those studies performed a profound analysis on a few datasets, we think a superficial comparison on a large number of experimental datasets is more important than a profound one on a few experimental datasets when estimating the methods' practical ability to detect DEGs, as the superficial comparison on a large number of datasets can also prevent selection bias regarding the datasets.
Additional information regarding each dataset, such as species composition and number of sequences is available at Table S1.
