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The genes activated by IL-28A and IL-29 comprised genes of immunity and defense (p = 5.7×10−17 for IL-28A, p = 2.5×10−16 for IL-29 vs. distribution of all genes on the microarray chip), especially interferon-mediated antiviral immunity (p = 2.1×10−7 for IL-28A, p = 1.8×10−6 for IL-29) and proteolysis (IL-28A only, p = 3.8×10−6) (Table 5; Fig. S1A).
Latitude was not significant in full models combining all 34 species but it interacted significantly with range for all principal components (P < 0.05), except defense (P = 0.930).
As expected, the Quarter Horse had more genes containing SNPs for each BP class, except for the immune and defense (P = 2.4 × 10-27) anucleiceic acid metabolism (P = 1.1 × 10-11) pAdditionaldditional file 34, Figure S8C, Additional file 35, Tables S27 and Additional file 36, Table S28).
Gene Ontology analysis (Ashburner et al., 2000; Huang et al., 2009a, 2009b) showed that editing targets are enriched for genes that encode zinc-finger proteins (p < 0.05), as well as proteins that are involved in chromosomal organization (p < 10−5) and antiviral defense (p < 10−3).
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GO enrichment analysis shows that carbohydrate metabolic process (p-value = 3.6E-4), transport (p-value = 4.1E-10) and defense (p-value = 6.3E-3) are overrepresented.
Chromosome 10 is enriched in the functional category "disease, virulence, and defense" (P-value 0.04) and chromosome 11 in the category "secondary metabolism" (P-value 0.04), followed by "virulence, disease factors" (P-value 0.06).
We tend to recalibrate apparent violations of LNC as conforming to a version of the law that incorporates the Aristotelian qualifications: a sincere defense of "p and not-p" plausibly involves a change in the context of evaluation or a shift in viewpoint, or alternatively a suppression of modal or epistemic operators.
According to our analyses, genes overlapping the regions of Landrace genomes that have an origin in Chinese breeds are enriched for immune-related GO terms, including "defense response" (p = 8.7 × 10-11), "response to virus" (p = 5.6 × 10-6) andefensense response to bacterium" (p = 0.012).
Both defense response (p = 6.22 e-08) and carboxylic acid processes (p = 8.17 e-05) were selected with significantly high probabilities.
In this analysis only two categories were over-represented, namely "defense response" (p = 4.14 × 10-9) and "response to biotic or abiotic stress" (p = 1.75 × 10-7).
In addition, genes in module M20 are enriched in the defense response (P = 0.047, after FDR correction), genes in module M18 are enriched in proteolysis (P = 0.035, after FDR correction), and genes in module M46 are enriched in photo transduction (P = 1.06e-23, aFDRr FDR correction) (Additional file 21), suggesting that lncRNAs may have regulatory roles in these processes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com