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Pancreas and renal morphological features were analyzed to refine phenotype characterization of BN.GK-Nidd/gk1 congenic rats in relation to diabetes and cardiovascular traits mapped to rat chromosome 1 QTLs.
The reads were first mapped to rat miRNAs using bowtie [ 45] without allowing for mismatches.
In particular, two blood pressure QTLs have been mapped to rat chromosome 2 [37].
Comparatively, 160 potentially associated SNPs mapped to rat mammary cancer susceptibility loci compared to 44 SNPs that mapped to random rat regions.
Those identical RNA tags were mapped to rat genome (Baylor 3.4/rn4) by SOAP software (Short Oligonucleotide Alignment Program, http://soap.genomics.org.cn) to analyze the expression of corresponding small RNA genes and their distribution on the genome.
Interestingly, 10 of these genes were found to be located in chromosomal regions that mapped to rat and/or human QTLs previously reported to be associated with inflammation, arthritis, or autoimmune diseases, such as systemic lupus erythematosus, multiple sclerosis, allergic rhinitis and asthma (Table 3).
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To determine if human GWA study-identified polymorphisms map to rat mammary cancer loci more frequently than to random regions of the rat genome, we selected rat genome segments that have not shown an association with mammary cancer risk.
There was a significant difference between the number of GWA study nominated SNPs mapping to rat Mcs/Mcsm loci compared to random rat regions in studies analyzing populations of European descent (66 SNPs to 51 SNPs respectively, P-value <0.05).
However, nearly 40% of genes differentially expressed between diabetic rats correspond to ESTs and predicted genes, which lack unambiguous annotation but represent attractive DN candidates, in particular when they map to rat chromosomal regions conserved with DN susceptibility loci.
A threshold of associated or potentially associated was used as the independent variable and outcome was either the SNP mapped to a rat mammary cancer locus or it mapped to a random rat region.
Several rat mammary cancer loci overlap extensively and subsequently several human polymorphisms mapped to multiple rat loci.
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