There are a wide variety of phenotypically and functionally heterogeneous monocyte subpopulations varying in maturation, differentiation, and activation states based on their differential expression of these surface markers (Auffray et al., 2009; Buckner et al., 2011; Shi and Pamer, 2011).
To identify such genes, we determined the rank product score for differentially expressed genes and classified them based on their differential expression in all 3 stages.
To increase the relevance of the predicted targets to DCs we further filtered them based on their differential expression in DCs relative to monocytes during DC differentiation using previously published data by Lehtonen et al (2007) [ 47].
Based on their differential inhibition of the three helicases, the inhibitors were classified into one of two groups: Inhibitors that had approximately equal effects on all three helicases include MAL2-11b and compounds 125248, 924384, 268973 and 388612 (Table 1).
In contrast with these previous studies, our method to detect stem-like cells was based on their differential responsiveness to a Sox2 reporter.
To conclude, our study has identified a subset of stem-like cells in NB based on their differential response to a Sox2 reporter.
The identification of the stem-like cell population based on their differential responsiveness to the Sox2 reporter has been demonstrated in a number of cancer models.
Based on their differential expression, an in vitro assay was developed to identify chemicals as sensitizing or not.
GSEA was performed with a list of pre-ranked genes based on their differential expression between the two groups using the GSEA pre-ranked function in the Gsea-3.0 software against C7 immunological signatures in the Molecular Signatures Database (MSigDB) v6.1.
Note that ranking scores for genes are based on their differential expression between untreated and drug treated samples.
In the first approach, we used microarray expression data of cells treated with drugs and diseases to rank genes based on their differential expression capability.
