Systematic interpretation of genetic interactions using protein networks

By Ryan M. Kelley, Trey Ideker. Nature Biotechnology, 2005

479 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c9044409e5f33d80d3a5f978a329373152a6e279

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Citations in the corpus

Mapping pathways and phenotypes by systematic gene overexpression. (2006, background): “The resultant complex genetic networks define gene function and map functional relationships amongst genes and pathways (Kelley and Ideker, 2005; Tong et al., 2004; Zhang et al., 2005).”
Comparative Genomics in Eukaryotes (2005, background): “, 2004), as well as gene fusion, conserved gene neighborhood and gene co-occurrences or phylogenetic profiles are indicative of both physical as well as metabolic interactions (Huynen et al., 2000; Jensen et al., 2004; Kelley and Ideker, 2005).”
Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems (2016, background): “…between complementary modules, whereas positive interactions tend to occur within a single module (Bandyopadhyay et al., 2008; Collins et al., 2010; Kelley and Ideker, 2005; Leiserson et al., 2011; Ma et al., 2008; Qi et al., 2008; Ulitsky et al., 2008); a more recent report identified dense…”
MIPS: analysis and annotation of proteins from whole genomes in 2005 (2006, methodology): “An important contribution of novel experimental techniques during the last few years has been the computational analysis of modules and networks based on the combination of independent types of information (4,5).”
MIPS: analysis and annotation of proteins from whole genomes in 2005 (2005, methodology): “An important contribution of novel experimental techniques during the last few years has been the computational analysis of modules and networks based on the combination of independent types of information (4,5).”
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. (2005, background): “However, because SSL interactions are most often found between genes involved in distinct processes (Kelley and Ideker, 2005), interpretation of the cause and significance of such interactions is often challenging.”
Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes (2015, unknown): “2013) has been used in the functional annotation of protein interaction networks (Kelley and Ideker 2005; Sharan et al. 2007) and in statistical modeling of complex social networks (Latapy et al.”
Network-based global inference of human disease genes (2008, background): “One possible explanation is the between-pathway hypothesis (Kelley and Ideker, 2005) that the two genes within an interacting pair come from different pathways compensating each other, with BRCA1 as the communication center, or the pivot node (Ulitsky and Shamir, 2007).”
Network-based prediction of protein function (2007, methodology): “Table I A summary of functional annotation methods”