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An automated method for finding molecular complexes in large protein interaction networks
TLDR
A novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes is described.
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Integration of biological networks and gene expression data using Cytoscape
TLDR
This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
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The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
TLDR
The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make Gene MANIA a useful tool for any biologist.
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The Genetic Landscape of a Cell
TLDR
A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function.
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Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
TLDR
A method for systematic construction of double mutants, termed synthetic genetic array (SGA) analysis, in which a query mutation is crossed to an array of ∼4700 deletion mutants is developed, which should produce a global map of gene function.
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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
TLDR
Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies.
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Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
TLDR
This work developed “Enrichment Map”, a network-based visualization method for gene-set enrichment results that is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software and is a significant advance in the interpretation of enrichment analysis.
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A travel guide to Cytoscape plugins
TLDR
A travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8 and ongoing efforts to distribute, organize and maintain the quality of the collection.
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Functional impact of global rare copy number variation in autism spectrum disorders
TLDR
The genome-wide characteristics of rare (<1% frequency) copy number variation in ASD are analysed using dense genotyping arrays to reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
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Global Mapping of the Yeast Genetic Interaction Network
TLDR
Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.
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