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These data suggest that the synergy between Grb2 and Dvl2 is likely direct, and depends on their physical interaction rather than the upregulation of an intermediary gene product.
Interestingly, we found that the C1-FFL architecture with a combinatorial logic type XOR (i.e., the activators inhibit each other) and a weak activation from the intermediary gene to the output is also a solution.
Therefore, a logical further step concerning adaptiveness would be to study the addition of more regulations over single FFLs, the effect of diffusion and the signaling at the intermediary gene level to obtain a widespread analysis of the different genetic architectures that allow reading gradients and generate one-stripe patterns.
Several modules were found to contain little or no connections to the rest of the network (i.e. stand-alone modules), representing genes whose expression is not linked to any other module either directly or via an intermediary gene.
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That is, rather than viewing the GPM as a list of genes with arrows pointing directly from each gene to a trait, some genes have arrows pointing to other genes, which may point directly to the trait, or may point to other intermediary genes before the path arrives at the trait.
A scientific challenge based on this hypothesis is to identify such putative intermediary genes and pathways in regenerating organisms.
Results: Explicit relationships between genes and diseases are formulated as candidate gene definitions that may include intermediary genes, e.g. orthologous or interacting genes.
Recently, Bai and colleagues conducted an ENU-based screen to identify suppressors of defective erythropoiesis resulting from a mutation in the gene encoding transcriptional intermediary factor 1-γ (TIF1γ; also known as TRIM33).
In previous work, Evi32 was believed to affect flanking gene nuclear receptor coactivator 2/transcription intermediary factor 2 (NCoA2/Tif2) [6], [7], [7].
In contrast to DNA, where the predominant role is the storage of genetic information, the biological role of RNA varies; ranging from a template-based intermediary in gene expression to playing a direct role in catalysis.
Among the genes in this category, 43% and 33% were assigned to amino acid biosynthesis (9/21 genes) and central intermediary metabolism (7/21 genes), respectively, and 14% (3/21 genes) were included in biosynthesis of cofactors and carriers.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com