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Guided by the proteomics data, experiments were designed to overcome the apparent limitation in amino acid accumulation capacity in GCDM-grown cells.
A PDS is a pathway-derived and biologically coherent feature determined by the proteomics data.
PDIA3, also known as ERp57, was chosen for our validation experiments because of its multiple functions in the processes identified by the proteomics data set.
Thus, an alternative mechanism supported by the proteomics data is that changes in the synthesis and breakdown of proteins (protein metabolism) may affect lifespan.
A comparison of the new start sites for the 47 genes proposed by the proteomics data to the start sites for the same 47 genes in the refined STM14028 genome annotation revealed an overlap of 34 genes where start sites matched exactly (Additional file 1 Table S3B).
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Gene expression can be followed throughout grain-fill by using the proteomics data to identify candidate genes to follow in a transcriptomic study.
Even so, there were three examples of probable false-negative findings that were revealed by considering the proteomics data in light of iSR215 (see discussion of fumarate hydratase, ribulose-5-phosphate 3-epimerase, and glucose-6-phosphate 1-dehydrogenase, above).
For further data analysis by means of multivariate statistics, the proteomics data as well as the Bio-Plex™ data were combined in a single data matrix and subjected to principal component analysis (PCA).
The high reproducibility of the proteomics data obtained by 2D-DIGE was reflected by a low variability of the quantified spots (median CV was 9.7% for all protein spots contained in Table 1).
We corroborated the miRNA target sites identified by PAR-CLIP [ 13] with the proteomics data [ 6, 7].
The proteomics data presented were processed by the Instrument Development Laboratory at the Environmental Molecular Sciences Laboratory (EMSL).
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