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The regulation analysis was performed on the bioinformatics predictions of TF binding sites and microRNA targets.
It may be interesting to further exclude known noncoding RNAs, transcription factor binding sites and microRNA binding sites in a future study.
Given the consequences of transcriptional complexity (alternate domain content, differential transcription factor binding sites and microRNA binding sites from alternative promoter and 3'UTR usage, respectively), understanding the complete repertoire of transcripts is crucial for accurate modelling of kidney organogenesis.
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The benefits of our framework are exemplarily shown in the context of phylogenetic profiling of transcription factor binding sites and detection of microRNAs close to transcription start sites of our gene set.
Here, we describe in detail analysis approaches for junction microarrays and provide suggestions for further analyses to delineate transcript level effects of the observed alterations as well as detection of microRNA binding sites and protein domains in the alternatively spliced target regions spanning across both untranslated and the coding regions of the targets.
The lentivirus vector lacked the normal c-myb 3'-UTR and the microRNA binding sites, and had its own promoter that was not subject to the complicated controls regulating expression of the endogenous c-myb gene.
These databases have been created to facilitate functional analyses by integrating multiple data sources such as expression, chromatin markups, microRNA binding sites and mutational data with known lncRNAs.
The observations are concordant with the speculation that mutant alleles of the two SNPs create microRNA binding sites and lead to repression of the MEFV gene.
Since 3' UTR contain microRNA binding sites and other stability determining regions, identification of the full length 3' UTR is important to elucidate posttranscriptional regulation.
Bioinformatic analyses of gene expression microarray data from fetuses exposed and unexposed to alcohol have examined upstream regulatory regions for common transcription binding sites and 5' untranslated regions for potential microRNA (miRNA) binding sites for differentially expressed genes.
The effective host microRNA response elements (MREs) have been incorporated into a virus sequence mainly based on the experimental trials for identifying both microRNA binding sites and effective mutations.
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