celegans_genetic_byrne — C. elegans genetic interaction similarity (2007)
- Description
Weighted network of similarity among genes of the nematode Caenorhabditis elegans, derived from the systematic genetic interaction analysis (SGI) of A. B. Byrne and collaborators. In that study, 11 "query" strains carrying mutations in conserved signal transduction pathways were each combined with the RNA interference (RNAi) knockdown of hundreds of "target" genes, and a genetic interaction was inferred when a mutant-RNAi combination grew more slowly than expected. The data were compiled by M. Cantor and collaborators for a study of nestedness across levels of biological organization, and are distributed in the repository of that study (file
mol_genes_celegans.txt). Using the interactions as given in the BioGRID database, they projected the query-target interactions onto the 454 target genes: nodes are target genes, and an undirected edge connects two target genes that interact with at least one common query gene, weighted by the Simpson index of their sets of interacting query genes (the number of shared query genes divided by the smaller of the two numbers of query genes each target interacts with), which ranges from 0 to 1. The genes are not identified in the source data.The edges have the property
weight, the Simpson index.
- Tags
- Biological Genetic Weighted Projection
- Citation
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- A. B. Byrne, M. T. Weirauch, V. Wong, M. Koeva, S. J. Dixon, J. M. Stuart, P. J. Roy, "A global analysis of genetic interactions in Caenorhabditis elegans." Journal of Biology 6, 8 (2007) 10.1186/jbiol58 Sci-Hub
- C. Stark, B.-J. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, M. Tyers, "BioGRID: a general repository for interaction datasets." Nucleic Acids Research 34, D535-D539 (2006) 10.1093/nar/gkj109 Sci-Hub
- M. Cantor, M. M. Pires, F. M. D. Marquitti, R. L. G. Raimundo, E. Sebastián-González, P. P. Coltri, S. I. Perez, D. R. Barneche, D. Y. C. Brandt, K. Nunes, F. G. Daura-Jorge, S. R. Floeter, P. R. Guimarães Jr., "Nestedness across biological scales." PLoS ONE 12(2), e0171691 (2017) 10.1371/journal.pone.0171691 Sci-Hub
- Upstream URL OK
- https://bitbucket.org/maucantor/unodf_analyses
- Networks
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Tip: hover over a column header for a description.
Column legend
- $\left<k\right>$
- Mean degree
- $\sigma_k$
- Standard deviation of the degrees
- $\lambda_h$
- Largest eigenvalue of the Hashimoto (non-backtracking) matrix
- $\tau$
- Random walk mixing time
- $r$
- Degree assortativity
- $c$
- Global clustering coefficient
- $\oslash$
- (Pseudo-) diameter
- $S$
- Relative size of the largest component
- NPs
- Node properties
- EPs
- Edge properties