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Whereas Relief-F find 13/17 and reGAIN + CINC find 5/17 main effect genes.
Among treatment main effect and time main effect genes 10 and 16 categories were overrepresented, respectively (Additional file 7).
Each of the terms enriched among treatment main effect genes was included in the enriched time main effect terms.
For each main effect, genes and exons with a Bonferroni corrected p-values of less than 0.01 were identified as differentially expressed.
The simulations are similar to the differential co-expression simulations but instead of varying the correlation noise, we increase the effect size of the 10% of main effect genes up to 2-fold.
For 8,609 (55%) of 15,575 time main effect, 3,826 (58%) of 6,266 treatment main effect genes, and 14 (61%) of 23 treatment by time interaction genes at least one GO term was assigned (Additional file 4).
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Using admixture mapping, we recently identified MYH9, encoding non-muscle myosin IIA heavy chain, as a main effect gene for idiopathic focal segmental glomerulosclerosis (FSGS) and HIV-associated nephropathy (HIVAN), which manifests as collapsing glomerulopathy, and as a risk predictor for end-stage kidney disease attributed to hypertension (H-ESKD) in the AA population (2).
In addition to these main effects (genes as a group or tissues as a group), significant variation could be attributed to the gene-tissue interaction effect (F1680,5669 = 38.55, p<0.0001), reflecting gene specific deviations in expression across various tissues.
We applied this method to successfully identify the main effect and gene-gene interactions for the phenotype "height" with the full set of KARE samples.
It is important to note that the complete genetic model will likely include main effects, numerous gene-gene and gene-environment interactions Nonetheless, in some cases we are able to explain more than 2% of the variability in protein levels just by focusing on two-locus interaction terms.
Logistic regression analysis was used to examine the main effect and gene-to-gene interaction of the 5-HTTLPR and 5-HT1B G861C polymorphisms for the risk of antisocial alcoholism.
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