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Although considerably more genes were differentially expressed in response to LIST LPS, similar molecular pathways and transcriptional networks were activated by the two LPS preparations.
Multiple genes were significantly (p<0.01, at least two-fold) differentially-expressed between these stages (Table S5), when considerably more genes were upregulated (1908 probe sets, 1509 mapped genes) than downregulated (432 probe sets, 301 mapped genes) in the later stage compared to the earlier one.
However, in some of our samples, considerably more genes are differentially expressed.
Our microarray results reflect this to some extent, with considerably more genes downregulated in the liver than upregulated.
Additionally, considerably more genes are repressed than activated, and primarily pathways connected with RNA processing are strongly repressed under stress conditions.
However, ANOVA did reveal that considerably more genes were altered in their expression due to the mouse background (493 genes) compared to chance alone (p < 0.01).
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above; [ 27]) in the embryo dataset displayed homogeneous gene expression, one would still expect to detect considerably more significant genes if the proportion of significant genes in the embryo data was identical to that in the juvenile data.
Non- bilaterian metazoa contain considerably more Sox genes [ 7, 8] indicating Sox gene loss has been important in the evolution of the bilateria.
Although differential loss and HGT can always be invoked as alternative explanations to each other, each scenario becomes increasingly less likely if it requires considerably more corresponding (gene loss or HGT) events [ 19, 21].
The results of this cluster analysis revealed that considerably more differential gene expression was detectable between the transcriptomes of Hdac1ATG1 and Standard Control morphant embryos at 12 hpf and 18 hpf, than was detectable at 27 hpf, even though there are no appreciable morphological abnormalities in Hdac1ATG1 morphant embryos before 22 hpf.
Our recent analysis of COI1-dependence of K-responsive genes indicates that the same is true here, but we identified considerably more OPDA-responsive genes among COI1-dependent than among COI-independent K-responsive genes ([ 18], Supplemental material SI4B-E therein).
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