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However, gene multiplicity in glycosyl hydrolase family 35 (GH35), to which these proteins belong, implies diverse functions.
By treating genes and cancers as actors and events using social network analysis techniques, we found evidence of patterns in cancer and gene multiplicity landscapes.
In this study, the gene multiplicity, apparent evolutionary relationships and transcript expression of rice Bgal genes were examined, in order to predict their biological functions.
Like other glycosidase families, GH35 includes multiple genes in various plant species, including Arabidopsis [ 12], tomato [ 13], papaya [ 14], apple [ 15], Vigna unguiculata [ 16] and barley [ 17], suggesting that GH35 gene multiplicity is ubiquitous in plants.
The generation of the clusters involves several steps: construct two-mode cancer and gene network, produce one-mode gene network and one-mode cancer network, calculate gene multiplicity values, generate Kamada-Kawai two-dimensional plane, compute 3D similarity matrix, and find hierarchical clusters.
In the best-studied cases, this leads to the selection of simple sequence repeats that generate variability at the promoter or at the protein sequence level [44], to selection for gene multiplicity for gene conversion between homologous sequences [45], or to signs of positive selection [46].
Similar(54)
Similar to Experiment 1 for gene maximum multiplicity, the cancer maximum multiplicity value for a cancer type is obtained from its maximum value link to any cancer type in the graph.
This is only a 0.01 improvement over the one-dimensional gene maximum multiplicity clustering, so gene maximum multiplicity is the primary measure generating the clusters that differentiate germline mutations from non-germline mutations.
In Figure 1, Genes c and d are more similar to each other, with a gene link multiplicity value of 2, than Genes a and b, with a gene link multiplicity of 1. Consequently, Genes c and d would be closer to each other in the two-dimensional space solved for minimum energy.
For example in Figure 1, a gene maximum multiplicity value of 2 is listed inside all the nodes since each node has a maximum multiplicity link of magnitude 2. Specifically, gene maximum multiplicity (Eq. 1, GeneMaxMultiplicity) and gene link multiplicity (Eq. 2, GeneLinkMultiplicity) are defined as follows.
Overall, genes with high gene maximum multiplicity scores were significantly more likely to be causal genes than those with lower gene maximum multiplicity scores (two-sample Kolmogorov-Smirnov test, one-tail, D34, 455 = 0.632, p < 0.05).
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