ArticleNature protocols2011
Assembling global maps of cellular function through integrative analysis of physical and genetic networks.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- High-Throughput Quantitative Genetic Interaction Mapping in the Fission YeastCold Spring Harbor protocols · 2018Article
- The recurrent architecture of tumour initiation, progression and drug sensitivity.Nature reviews. Cancer · 2017Review
- Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis.Evolutionary bioinformatics online · 2016Review
- Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms.BMC bioinformatics · 2015Article
- Detection of composite communities in multiplex biological networks.Scientific reports · 2015Article
- Unifying immunology with informatics and multiscale biology.Nature immunology · 2014Review
- Porting and using PanGIA for Cytoscape 3: challenges and solutions.F1000Research · 2014Article
- A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring.Cell reports · 2013Article
- Integrative approaches for finding modular structure in biological networks.Nature reviews. Genetics · 2013Review
- Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.Pharmacology & therapeutics · 2013Review
- Dissection of DNA damage responses using multiconditional genetic interaction maps.Molecular cell · 2013Article
- Modular biological function is most effectively captured by combining molecular interaction data types.PloS one · 2013Article
- Differential analysis of high-throughput quantitative genetic interaction data.Genome biology · 2012Article
- A travel guide to Cytoscape plugins.Nature methods · 2012Article
- Topological analysis and interactive visualization of biological networks and protein structures.Nature protocols · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies 'modules' as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules. This protocol begins with importing interaction networks into Cytoscape, followed by filtering and basic network visualization. Next, PanGIA is used to infer a set of modules and their functional inter-relationships. This module map is visualized in a number of intuitive ways, and modules are tested for functional enrichment and overlap with known complexes. The full protocol can be completed between 10 and 30 min, depending on the size of the data set being analyzed.
Indexed as
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.