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The functional assignment of the genes with decreasing expression by GO clustered them in the processes of localization (p-value = 10e−4) (Table S4, S 18).
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The follow-up gene ontology (GO) clustering analysis using DAVID (Huang et al., 2009) revealed that genes associated with 'neurogenesis', 'neuron differentiation' and 'metamorphosis' were markedly enriched among transcripts downregulated in ras V12scrib tumors (Fig. 1C, supplementary material Table S1).
There were 64694 unigenes showing differences in transcript abundance, and 5032 were defined as DEGs using the thresholds of false discovery rate (FDR) ≤ 0.001 and |log2Ratio| ≥ 1. GO clustering analysis suggested the potential biological functions of these DEGs.
Although a negative going significant cluster appeared for both the slowed down sequence and the strong AM stimulus condition around 100 110 ms, the earlier positive going cluster existed only in the strong AM stimulus condition (Diff(AM)).
But when asked how things were going, everyone clustered round and began to shout.
There is clearly a need to go beyond clustering to analyze MD folding trajectories.
GO cluster were found using GO term finder option in www.candidagenome.org.org
The GO clusters that were most significantly downregulated in all data sets were again related to DNA repair, cell cycle, and mitosis as described before for cells undergoing DISE24.
Multiple GO clusters were not assigned to one of these categories due to lack of coherence.
GO clusters with an enrichment score greater than 1.3 were considered significant [35], [36].
In the cortex, 81 GO clusters were formed but only 15 of them showed an enrichment score greater than 1.3.
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