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Signal transduction pathways associated with gene expression changes were analyzed and defined using the bioresource for array genes (BioRag, www.biorag.org).
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In addition, the CHARGE Study seeks to evaluate gene × environment interactions and to analyze phenotypic subtypes defined using behavioral or physiologic criteria, in order to determine whether environmental factors are more strongly related to specific subsets of autism cases.
We combined and analyzed migrant sub-groups defined using UN macro-regions (see Additional file 3) or country of origin, migration status, and length of time in receiving-country.
In addition, the three sub-groups analyzed (normal mPAP, BoPAP and PAH) were defined using mPAP (a continuous variable).
Reads mapping to filtered peaks were tabulated into a matrix and analyzed using edgeR [ 11] and statistical significance defined using a false discovery rate of 0.1.Functional analysis of DMRs was performed with DAVID [ 12, 13] using default parameters.
An overall analysis was performed with the duration of time spent in a smoky cabin analyzed as a continuous variable and a supplemental analysis was performed with duration of time spent in a smoky cabin analyzed as a categorical variable with categories defined using quartiles of the observed distribution (≤11030 hours, 11031 to 18240 hours, 18241 to 27750 hours, and ≥27751 hours).
Progeny of individual clones were then analyzed with respect to particular regional boundaries defined using appropriate GAL4 lines or other region-specific markers.
Structural relationships were defined using ultrastructural and morphometric approaches while transparency was analyzed using in vivo confocal microscopy.
Pixel overlap between binary red and green images in the remaining cell regions was defined using the 'Boolean operations' module and further analyzed using Excel (Microsoft, Redmond, WA).
Abnormal paired-end alignments were analyzed by clustering and comparing with the types of structure variation previously defined using the software Breakdancer [ 20] run using the default parameters.
These three risk tiers were defined using only progression status at 2 years and 4 years after analyzed specimens were obtained.
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