The impact of genetic interaction networks on evolution is a fundamental issue. Previous studies have demonstrated that the topology of the network is determined by the properties of the cellular machinery. Functionally related genes frequently interact with one another, and they establish modules, e....
This method generates a large number of double mutant combinations, and has been successfully used to identify genetic interaction networks in yeast in a wide range of cellular processes [12, 13, 20, 21]. In the budding yeast Saccharomyces cerevisiae, 32 genes encode predicted or demonstrated ...
et al. A global genetic interaction network maps a wiring diagram of cellular function. Science 353, pii: aaf1420 (2016). Baryshnikova, A., Costanzo, M., Myers, C. L., Andrews, B. & Boone, C. Genetic interaction networks: toward an understanding of heritability. Annu. Rev. Genom. ...
A-X, A-Z, B-X, B-Y, B-Z) (Fig.1b). This model for the local topology of genetic networks, called the “between-pathway model” (BPM), has been widely observed in yeast genetic interaction networks11,14. Indeed, as many as ~70...
Functional interaction networks were constructed using the ReactomeFIViz App (ReactomeFIViz app and Reactome FI Network, Wu and Haw 2017 PMID: 28150241) in Cytoscape (v3.6.1) [29]. GWAS-FI network was constructed using nearest genes to each of the 71 GWAS loci. SMR FI network was construct...
Recent advances in post-genomic biology are enabling us to investigate and reconstruct the precise gene interaction networks. Inferring genetic networks from a large-scale expression data is very important to understand the underlying biological systems. Thus in this paper, we review the state of the...
(MGED), nonlinear modeling of these interactions is now feasible. Two of the latest advances in nonlinear modeling used sigmoid models to depict transcriptional interaction of a transcription factor (TF) for a target gene, but do not model cooperative or competitive interactions of several TFs for...
When using GRETTA, please cite the manuscript describing GRETTA: Yuka Takemon, Marco A Marra, GRETTA: an R package for mapping in silico genetic interaction and essentiality networks, Bioinformatics, Volume 39, Issue 6, June 2023, btad381,https://doi.org/10.1093/bioinformatics/btad381 ...
Different from APN that drew network sample from complete network, our method introducing protein interaction networks as underlying pathway structures. In addition, a scoring function is defined by gene pairwise score, which can avoid the unadjusted balance between gene pairwise score and edge score...
genetic interaction and directionality scores for each gene pair. Based on the results from over 100,000 perturbed gene pairs, we reconstruct a directional dependency network for human K562 leukemia cells and demonstrate how our approach allows the determination of directionality in activating genetic ...