Exact(1)
Because of late RNA extraction (48 hours after LPS stimulation) we did not expect to see differentially expressed gene that display an early and transient response during the macrophage activation process [38].
Similar(59)
Although the number of patients who expressed a cytokine/chemokine expression signature is small (four out of 20), the genes seen differentially expressed in this subgroup suggest that alteration in innate rather than adaptive immunity may play an important role in the pathogenesis of SLE in a subset of patients.
Although miR-34a was previously shown to regulate TP53, we do not see it differentially expressed in the context of TP53 mutational status which might indicate a lack of feedback loop in this regulation.
However, we do want to see most differentially expressed genes appearing on both lists.
According with the definition given in Materials and Methods, 3,056 probe sets were found to be differentially expressed (see additional file 1: Differentially expressed genes under drought conditions).
Insulin, antihypertensives, and cholesterol medication were seen as differentially helpful for diabetes and for preventing heart disease, indicating that patients hold specific beliefs about each medication type in ways that make intuitive sense.
Interestingly, while we report increased abundance of bacteriorhodopsin, halorhodopsin and genes involved in arginine metabolism/fermentation in stationary phase, these are not seen as differentially abundant in Lange et al. These processes have conventionally been associated with stationary phase-like physiology [ 13, 28].
Expression of KIR receptors is complex and controlled by a stochastic mechanism that shuts off expression of some receptors and not others in individual cells thereby allowing different NK cell clones to recognize their targets differentially (see review: [6]).
Given the sense-antisense architecture of the microarray (see above), all differentially expressed microarray targets were examined to identify and eliminate microarray targets for which both the sense and antisense probes were differentially expressed.
In addition, we also used expression profiling of each of the diseases, to see if genes differentially expressed in the disease were enriched for binding sites of the predicted TF (See Supplementary Materials for details).
For the comparative analysis genes with high quality values in the two experiments (see above) and differentially expressed between Hz and Od and between highly sensitive (S) and less sensitive (LS) pools after one week of cold storage were selected.
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