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Furthermore, we used microarray data stemming from lung tissue of a mouse transgenic line overexpressing the oncogene c-myc.
We used four different microarray data stemming from compound-treatment experiments: human hepatocytes treated with 1) Aroclor 1254, as published recently [ 8], with 2) trovafloxacin [ 15], with 3) doxorubicin, and with 4) etoposide [ 9].
Notably, by using microarray data stemming from lung tissue of a mouse transgenic line overexpressing the transcription factor c-myc, which served as a negative control, we found regulated genes to be located with regard to each other nearly in the same way as genes distributed randomly all over the genome (0 100 kbp).
In this study, we were able to reproduce this observation with microarray data stemming from 1) human hepatocytes treated with the gyrase and potential topoisomerase II inhibitor trovafloxacin, 2) human hepatocytes treated with the topoisomerase II inhibitor doxorubicin and 3) mouse lymphoma cells treated with the topoisomerase II inhibitor etoposide.
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Third, the authors suggest, in the Conclusions, that the popular notion of the prohibitive noisiness of microarray data stems from the deterministic view of biological data, in other words, disregard of intrinsic, biological noise (to me, this looks like better terminology than that used by the authors).
The curve arising when expression levels are estimated from abundance within the EST database, Figure 2, shows an unexpected non-monotonic behavior, increasing in the region of lowly expressed genes and decreasing in the region of highly expressed genes, in evident conflict with the data stemming from microarray experiments.
Further, the control probes were left out of the meta-analysis, as this was also done for the data stemming from the other microarray platforms.
Sullivan et al. [ 27] carried out a secondary analysis on data stemming from 79 human tissues for 33,698 genes (probed using the Affymetrix U133A microarray).
The latest available data stems from 2013.
Data stem from in situ experiments.
To find out the relationship between the gene expression shifts in the ams mutant and their expression preferences in different organs, we compared our data from wild-type anther with previous microarray data from roots, stems, leaves, seedlings, siliques and inflorescences.
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