ArticleScience signaling2013
Protein complex-based analysis framework for high-throughput data sets.
Article in Science signaling, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 124 citations in OpenAlex.
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- PANGEA: a new gene set enrichment tool for Drosophila and common research organisms.Nucleic acids research · 2023Article
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- PANGEA: A New Gene Set Enrichment Tool forbioRxiv : the preprint server for biology · 2023Article
- Next-generation large-scale binary protein interaction network for Drosophila melanogaster.Nature communications · 2023Article
- Identification of two pathways mediating protein targeting from ER to lipid droplets.Nature cell biology · 2022Article
- Regulation of protein abundance in genetically diverse mouse populations.Cell genomics · 2021Article
- mTORC1-chaperonin CCT signaling regulates mProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells.PLoS genetics · 2021Article
- FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update.Nucleic acids research · 2021Article
9 more citing papers are in PubMed but not listed here.
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 2 institutions in 1 country.
Funding
Abstract
Analysis of high-throughput data increasingly relies on pathway annotation and functional information derived from Gene Ontology. This approach has limitations, in particular for the analysis of network dynamics over time or under different experimental conditions, in which modules within a network rather than complete pathways might respond and change. We report an analysis framework based on protein complexes, which are at the core of network reorganization. We generated a protein complex resource for human, Drosophila, and yeast from the literature and databases of protein-protein interaction networks, with each species having thousands of complexes. We developed COMPLEAT (http://www.flyrnai.org/compleat), a tool for data mining and visualization for complex-based analysis of high-throughput data sets, as well as analysis and integration of heterogeneous proteomics and gene expression data sets. With COMPLEAT, we identified dynamically regulated protein complexes among genome-wide RNA interference data sets that used the abundance of phosphorylated extracellular signal-regulated kinase in cells stimulated with either insulin or epidermal growth factor as the output. The analysis predicted that the Brahma complex participated in the insulin response.
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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.