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Most functional pathways involve interactions between genes across multiple families.
Although most functional pathways were similarly represented in E. bieneusi and other microsporidia, several exceptions stand out.
Specifically, most functional pathways present in other microsporidia are well represented in both E. bieneusi surveys, with the exception of all pathways relating to energy generation.
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The Functions tool in Ingenuity relates genes of interest to known biological functions and disease states and was used to detect the most significant functional pathways in the 'rescued' genes.
In addition, gene ontology analysis of mA-containing genes also revealed that the most correlated functional pathways are related to RNA metabolism [24].
The results indicate that the complex expression profiling of pathogen challenged pbMEC sampled from cows inheriting alternative QTL alleles is suitable to study genetically determined molecular mechanisms of mastitis susceptibility in mammary epithelial cells in vitro and to highlight the most likely functional pathways and candidate genes underlying the QTL effect.
We found high levels of many amino acids within the PCa bone metastases, and amino acid metabolism was the most altered functional pathway associated with PCa bone metastases according to Ingenuity pathway analysis.
IPA Ingenuity® Knowledge Base (Ingenuity® Systems) dataset analysis highlighted glycolysis or potentially the reciprocal gluconeogenetic metabolic pathway as the most affected functional pathway in the rWNT5A-treated A2058 cells.
The most significant (top) functional pathways highlighted by IPA consisted of 1) cancer, reproductive system disease, and genetic disorders and 2) cell death, hematological system development and function, and cancer.
Finally, combined domain analysis, evolutionary analysis and coevolutionary analysis reveal that most functional domains in Hippo pathway genes have not only been under purifying selection but also coevolved with interacting functional domains in other genes.
Two functional pathways were most significant: the cell adhesion through extracellular matrix remodeling (p = 4.964e−06), and MHC-class-I mediated antigen presentation (p = 9.843e−05).
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