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2. Detection limit of cDNA microarray analysis could prevent some expression changes to be detected.
Both studies demonstrated that altered miRNA expression in tumors was complex and involved distinct normal cell types and tumor compartments for different miRNAs; some expression changes suggested an etiological contribution of specific miRNAs, whereas others did not.
Despite significant ontological clusters, it is notable that the fold changes in genes in the clusters mentioned above were themselves very moderate by array, possibly explaining why only some expression changes were able to be validated by qPCR.
Therefore, while the possibility that some expression changes are due to differences in tissue handling cannot be formally ruled out, it is unlikely that the large and specific differences we observe in tumor v donor, tumor v adjacent normal and adjacent normal v donor are entirely due to processing differences.
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There are several pathways picked out by ambient that show some expression change and link between the metabolic pathways that have already been identified by others [ 3, 13] to change on diauxic shift in yeast.
We found some similar expression changes in at least some of the target organs, but that the majority of the early gene expression changes were tissue specific, as were some of the biological processes related to the modulated genes.
However, some gene expression changes induced by AR overexpression (gene downregulations) were further augmented by the treatment with the androgen ligand in these cells.
The potential adaptive significance of some gene expression changes has also been posited [ 6].
Another obstacle to selecting causal sensitivity/resistance genes is that some gene expression changes may serve as markers of resistance, but not contributing functionally to the phenotype.
The experimental and control strains shared some gene expression changes, which are likely loci responding to adaptation to the culture conditions and media.
Although no studies have been published to date on chromosomal variations related to malathion exposure, some gene expression changes after exposure to malathion in this study are similar to those found in other cell culture models of chromosomal changes (Geigl et al. 2004; Waisfisz et al. 2002).
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