ArticleNature protocols2009
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor.
Article in Nature protocols, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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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.
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Who cites it
4 citing papers in PubMed.
- HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions.BMC genomics · 2017Article
- Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes.Nature protocols · 2016Article
- Capturing cooperative interactions with the PSI-MI format.Database : the journal of biological databases and curation · 2013Article
- Missing and spurious interactions and the reconstruction of complex networks.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The systematic mapping of protein interactions by bait-prey techniques, including affinity purification-mass spectrometry or the yeast two-hybrid system, contributes a unique and relevant perspective on the comprehensive picture of cellular machines. We describe here a protocol for statistical analysis of node-and-edge graph representations of these data using R and Bioconductor, recognizing that steps may be added or omitted depending on the data set at hand. The fundamental purpose of such analyses is feature estimation, defined here as the estimation of data-type-specific biological features, such as protein complex composition and the physical interaction integrity of known or estimated complexes. In preparation for feature estimation tasks, we outline a progression through three analytic components common to all bait-prey data types: preliminary setup, exploratory analysis and quality assessment. The end result is a collection of descriptive and inferred characteristics of the data, ready for biological interpretation in a computationally tractable form.
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19325550What OpenQuestion holds
Registered trials
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