High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. This methodology is frequently used to validate predicted targets of microRNA b
Deletions of this type can often be attributed to genomic instability; typically this instability is associated with the formation of alternative, non-B DNA secondary structures [28]. As a general rule, DNA sequences that form such secondary structures are repetitive [28]; yet, analysis of the...
Data extracted included key characteristics regarding source, participant, test and key results and recorded in a data extraction form in Microsoft Excel. Categories and subcategories of the full data extraction form are listed in Appendix Table3. Data extraction from non-English language papers was ...
A particular type of network is gene regulatory networks (GRNs) that are comprised of regulators and their target genes. One type of regulators is transcription factors (TFs), regulatory proteins that bind to DNA to activate or repress gene transcription. TFs often form complexes that act ...
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form was also used to systematically collect all relevant clinical parameters during pregnancy, labor, and follow up visits. The questionnaires and clinical forms were only collected for the women participating in the prospective cohort study but not for the group of women that tested HPV-negative ...
(TableS2). A volcano plot was used to show the relationship between the adjustedp-value and log2FoldChange(Fig.3c). GO term enrichment and pathway enrichment analysis presented in the form of a bubble plot provided certain information (Fig.3d,e). The most enriched pathway was that of the...
1). In their simplest form, deletions and inversions were found to be the most common SV types, while consistent with other PCa studies, we observed a low frequency of insertion events (Additional file 1: Fig. S2). Only 15 tumours (8.3%) presented with at least one insertion, which may...
NLR-IDs in MIC1 form genetic pairs with NLRs from another clade The NLR-IDsRRS1andRGA5require a genetically linked partner NLRRPS4andRGA4, respectively, to be functional. Homologs ofRRS1/RPS4pair are also found in pairs [12]. We determined how many NLR-IDs from MIC1 and overall in ...
analysis, and only their direct targets in the co-expression modules are kept to form the regulons. Finally, binarized scores are calculated to indicate TF’s activity in each cell. The other methods, including SCODE [249] and SINCERITIES [250], take advantage of the pseudo-temporal ...