Discovering regulatory and signalling circuits in molecular interaction networks

By Trey Ideker, Owen Ozier, Benno Schwikowski, Andrew F. Siegel. Intelligent Systems in Molecular Biology, 2002

1,236 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/7155d2ff9b2d0daaf58847ae3985f23583425c87

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Citations in the corpus

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks (2012, methodology): “JActiveModules [10] is a popular and easy to use software, as it is run on the state-of-the-art network browser platform Cytoscape [11].”
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics (2007, background): “Protein–protein interaction networks and regulatory networks are the key representatives for biological networks with undirected and directed edges [7–12].”
Computational solutions for omics data (2013, background): “Early pioneering work, now implemented as the jActive modules plugin for Cytoscape 3 , introduced the concept of active subnetworks, which consist of connected regions in physical interaction networks that manifest significant expression changes in specific contexts 116 .”
Differential network biology (2012, methodology): “Someunderstanding of the dynamics of large networks has been achieved by integrating static interaction measurements with dynamic changes in gene expression or metabolic ﬂuxes (Ideker et al , 2002; Luscombe et al , 2004; Sauer, 2004; de Lichtenberg et al , 2005).”
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data (2015, methodology): “They include obvious aspects such as control versus treatment used in challenge studies, but when applied to a complex data set (e.g., humans with a specific disease) they can include demographic information about sex, weight,”
More Is Better: Recent Progress in Multi-Omics Data Integration Methods (2017, background): “It is another network-based Cytoscape plug-in which seeks underlying network hotspots through the integration of gene expression, protein-protein interaction, and protein-DNA interaction data (Ideker et al., 2002).”
Protein networks in disease. (2008, methodology): “Finally, there is a rich yeast literature on methods for integrating gene-expression data with molecular networks and pathways, with the goal of identifying network “hot spots” or “expression-activated modules” (Zien et al. 2000; Ge et al. 2001; Ideker et al. 2001, 2002; Hanisch et al. 2002).”