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Based on microarray datasets for three diseases, we show that though there are few genes shared between the DEG lists from different studies for a disease, most of the POGR and nPOGR scores are rather high, suggesting high reproducibility of the DEG lists in the sense that the apparently inconsistent DEG lists are significantly correlated.
No other signaling pathway gene lists are significantly up- or downregulated in spt for the 21-somite tail tissue (Wnt FDR q = 0.615, NES = 1.091; TGF-β FDR q = 0.609, NES = 1.000; Delta-Notch FDR q = 0.673, NES = 0.889; FGF FDR q = 0.793, NES = 1.173).
All DMR and VMR lists are significantly colocated in DNase 1 hypersensitivity hot spots from blood cell line data deposited by the ENCODE consortium specific for CD20 and CD34+ mobilized cell types, but not in TH1, GM06990 and GM12865 cell lines (Table 6 and Table S4).
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According to a report by Michael H. Thaut at Colorado State University, a study of patients with MS showed that word lists were significantly better learned and recalled when presented and rehearsed via song as opposed to standard spoken presentation and rehearsal.
We used the hypergeometric test to decide whether the overlap between the 117 diet-related genes and each of the 5'PS gene lists was significantly larger than expected, given the overlap between human and chimpanzee 5'PS genes and the three control sets defined above (see the Materials and Methods section "DNA sequence divergence").
This analysis finds that the number of common Biological Processes (derived without any FDR control) that we found for the real lists was significantly higher than the number for random signatures- we calculated a p-value of 0.015 to get the observed overlap for threshold of p<0.05 (and 0.068 for p<0.1), showing that indeed both signatures capture some common essence.
The adherence to available essential medicines lists was significantly lower at the NTH.
None of these most changed gene lists were significantly prognostic in two datasets [ 37, 38] of ER-positive tumors that did not receive adjuvant therapy.
Both these lists were significantly enriched for transcriptional control, RNA processing, and chromatin remodeling; these enrichments were particularly significant among the 97 proteins that were both predicted by the two techniques and experimentally confirmed as Cbf11 interactors.
Lastly, the pathway analysis performed on the 1000 genes that were most differentially expressed (500 genes upregulated in responders and 500 genes upregulated in nonresponders) demonstrated that these gene lists were significantly enriched in genes with different ontologies (additional Tables 6 and 7).
Listed are significantly enriched KEGG terms with cutoff of p ≤ 0.05.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com