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Additional file 2: List of Cellular Component Gene Ontology (GO) terms enriched between two consecutive developmental stages.
A comparative analysis was performed using SAM software to identify changes in expression profiles between two consecutive developmental stages [ 30].
Additional file 3: List of Encyclopedia of Genes and Genomes (KEGG) pathway components enriched between two consecutive developmental stages.
Principle component analysis (PCA) was analyzed by using R. Differentially expressed genes between two consecutive developmental stages were identified using default parameters in DESeq [ 52].
Of all of the KEGG pathways predicted to be involved in the comparison between two consecutive developmental stages, the tyrosine metabolic pathway (ko00350) was continuously active from the trochophore stage to juveniles with a q-value < 0.05.
Thus, we identified all genes involved in biomineralization in the oyster transcriptome, including the majority of known P. fucata matrix proteins like shematrin family, PFMG family, tyrosinase family and other proteins described before, and analyzed their expression profiles between two consecutive developmental stages [ 31- 38].
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This theory explains pulmonary hypoplasia by two consecutive developmental insults.
The current view presents hemangioblasts and hematogenic endothelial cells as two consecutive developmental stages leading to formation of blood [ 4].
The functional enrichment of up- or down-regulated genes during two consecutive developmental stages was assessed based on the GO [ 62] and KEGG [ 63] pathways annotation terms.
The two consecutive developmental stages were composed of berries sampled in clusters at and after the onset of ripening, as estimated by pericarp softening.
Consequently, temporally dynamic manipulation of extracellular signals was imperative to suppress the production of unwanted cell fates across six consecutive developmental junctures.
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