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We conjecture that the visualization of the expression behavior of a gene over the conditions of the compendium, together with the identification of the significant cultivation parameters to which the gene responds, provides valuable information regarding gene function.
This procedure is based on gene expression analysis and exploits the inverse correlation existing between the expression behavior of a host gene and the target genes of the corresponding intragenic miRNA.
Since the expression behavior of a module reveals under which combination of cultivation conditions the genes are up- or downregulated, we are not only able to relate TFs to the groups of genes that they presumably regulate, but also to the precise environmental conditions that trigger their activity to perform their regulatory role.
While traditional microarray experiments strive to establish the 'global view' of the activity of all genes (i.e., the genome) in response to environmental conditions, they may also be used to characterize and quantitatively describe gene expression behavior of a selected set of genes as a true genotypic correlate of a particular phenotype.
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Overall, our work suggests that the marked oscillating gene expression behavior of a-iPSCs during differentiation and their great number of mitochondria compared to y-iPSCs, reflects their intrinsic instability and failure to differentiate.
As well known to us, biclusters represent similar expression behaviors of a group of genes at the same time points.
The analysis of multiple X-linked loci in each sample revealed that the expression behavior of the chromosome as a whole may not be inferred from that of a single locus.
Second, it is based on a molecular signature that contains the collective expression behavior of gene groups, without a priori bias related to their biological affiliations.
Another gene with a large influence on the net expression behavior of the carotenoid biosynthetic pathway was a β-carotene hydroxylase (row 6 of Additional file 1: Table AF1-8, PAnel A of Additional file 1: Figure AF1-7), which showed an expression change from 42 TPM at 10 DAA to 1,709 TPM at 60 DAA.
A table showing expression behavior of double-cysteine mutants and supplementary figures.
EST information has been provided for a better understanding on the expression behavior of particular candidate genes.
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