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When growing on multi-carbon substrates, M. extorquens AM1 uses pathways that are common to many heterotrophs, including the TCA cycle, the pentose-phosphate pathway, parts of anapleurotic pathways and gluconeogenesis, and an electron transport chain involving NADH dehydrogenase [1], [11].
The latter uses pathways as an entry point of variant information through a pathway table browse function.
GSA typically uses pathways or functional categories of cellular processes to define gene sets, such as those from the KEGG database [ 3] and the Gene Ontology (GO) annotations [ 4].
This software uses pathways present in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and calculates significance, through hypergeometric distribution testing, based on the relative changes of the contained genes.
The first is identification of pathways significantly enriched in genes containing non-synonymous mutations; the second uses pathways so identified to find groups that are functionally related in the largest number of samples.
PANTHER uses pathways compiled by experts to find pathways that are overrepresented in a list of genes by comparing it to a reference list, e.g. all genes in the mouse genome as used here.
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A similar technique could be deployed in a more conventional garden, using pathways that lead visitors back on themselves, to ensure they experience all the views (mountephraimgardens.co.uk).
In its scope and character, it has been compared with other urban-suburban multi-use pathways, like the Minuteman Trail outside of Boston and the Crescent Trail that runs from Bethesda, Md., through Washington and to Mount Vernon, Va.
LLM students will use Pathways 4 or 5 to meet this requirement.
Cells might deal with PFTs using pathways that regulate cell death.
We use pathways as lists of genes in our approach.
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