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We identified PMEI as a NAC regulated potential candidate gene and the expression of PMEI gene is up-regulated by this NAC transcription factor, indicating that PMEI reduces the activity of PMEs during later stages of seedling development.
To obtain hints for how expression of the CaM genes may be regulated, potential cis-acting elements in upstream 1000 bp sequences of the SlCaM genes were analyzed.
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The Arabidopsis gene IDs associated with the corresponding soybean genes encoding these 2,938 differentially expressed transcripts were cross-referenced with the Arabidopsis ABA-related and FUS3-regulated genes to obtain ABA-related and FUS3-regulated potential homologs in soybean.
Among 9 enriched pathways, 5 pathways had more up-regulated DEGs; 3 pathways had more down-regulated DEGs; one pathway had a same number of up- and down-regulated potential stress-responsive genes.
These were up-regulated miRNAs and their potential down-regulated mRNA targets (39 and 299 respectively; Additional file 5); down-regulated miRNAs and their potential up-regulated mRNA targets (20 and 330 respectively; Additional file 6); and up-regulated miRNAs and their most highly up-regulated potential mRNA targets (15 and 41 respectively; Additional file 19).
In the IPA core analysis of the miRNA-regulated candidate gene lists (299 up-regulated and 330 down-regulated), the potential transcription factors were predicted (Additional files 15 and 16; Upstream Regulators).
And regulated harm potential.
To further investigate the global expression response to BSE infection and to define interactions among the identified specific pathways containing the regulated genes, potential networks of interacting DEGs were identified using IPA®.
For several groups of co-regulated transcripts, potential protein binding sites in the untranslated regions were found, which were conserved in different kinetoplastids.
For example members of the thaumatin family (2.8 fold down-regulated) have potential endo-β-1,3 glucanase activity [ 34].
Analysis of a novel GeneChip® dataset resulted in the identification of 1484 DEGs from the duodenum of iron-deficient rats at several postnatal ages, providing us with a unique opportunity to identify groups of induced genes that were potentially coordinately regulated and identify potential mechanisms that could be responsible for this common regulation.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com