The jury is out on 'guilt by association' trials

Semple, Jennifer I.; Sanderson, Christopher M.; Campbell, Rolla D.

doi:10.1093/bfgp/1.1.40

Cited by 13 publications

(9 citation statements)

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“…This is equivalent to an average of 4.5 interactions per bait, which compares favorably to the number of interactions per bait in genome-wide Y2H studies (∼1 interaction per bait; see Semple et al 2002), and thus demonstrates the additional information that can result from performing comprehensive pathway-focused interaction mapping studies in addition to genome-wide projects (Walhout et al 2000). As with the results of any high-throughput interaction assay, the interactions listed here should be considered as putative or predicted interactions.…”

Section: Interactions With Other Proteinsmentioning

confidence: 88%

“…As in previous M2H studies , no strong interactions were detected between Rrp6 or Rrp44 (which is exosome-associated in yeast) and other subunits. Sometimes a protein interaction is only detectable by Y2H using a fragment of a protein, because the full-length protein may not express well in yeast, or because an interaction only occurs when a conformational change in the full-length protein exposes a subdomain (Semple et al 2002). Therefore, for proteins where no interactions were detected using full-length constructs, protein fragments corresponding to predicted structural domains were used as Y2H baits and preys.…”

Section: Subunit Interactions Of the Human Exosome Complexmentioning

confidence: 99%

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A Protein Interaction Framework for Human mRNA Degradation

Lehner¹,

Sanderson²

2004

Genome Res.

126

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The degradation of mRNA is an important regulatory step in the control of gene expression. However, mammalian RNA decay pathways remain poorly characterized. To provide a framework for studying mammalian RNA decay, a two-hybrid protein interaction map was generated using 54 constructs from 38 human proteins predicted to function in mRNA decay. The results provide evidence for interactions between many different proteins required for mRNA decay. Of particular interest are interactions between the poly(A) ribonuclease and the exosome and between the Lsm complex, decapping factors, and 5Ј→3Ј exonucleases. Moreover, multiple interactions connect 5Ј→3Ј and 3Ј→5Ј decay proteins to each other and to nonsense-mediated decay factors, providing the opportunity for coordination between decay pathways. The interaction network also predicts the internal organization of the exosome and Lsm complexes. Additional interactions connect mRNA decay factors to many novel proteins and to proteins required for other steps in gene expression. These results provide an experimental insight into the organization of proteins required for mRNA decay and their coupling to other cellular processes, and the physiological relevance of many of these interactions are supported by their evolutionary conservation. The interactions also provide a wealth of hypotheses to guide future research on mRNA degradation and demonstrate the power of exhaustive protein interaction mapping in aiding understanding of uncharacterized protein complexes and pathways.

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Section: Interactions With Other Proteinsmentioning

confidence: 88%

Section: Subunit Interactions Of the Human Exosome Complexmentioning

confidence: 99%

A Protein Interaction Framework for Human mRNA Degradation

Lehner¹,

Sanderson²

2004

Genome Res.

126

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“…96 Therefore, an open access interaction viewer implemented as a Java Web Start plugin on top of the prefuse visualization toolkit (http://prefuse.org) enables dynamic browsing of our unified PPI data. This interactive tool is rich in features that facilitate the navigation through interaction maps which are regularly represented as a set of nodes connected by intermolecular edges.…”

Section: Primos Protein Interaction Network Visualization Toolmentioning

confidence: 99%

PRIMOS: An Integrated Database of Reassessed Protein–Protein Interactions Providing Web-Based Access toIn SilicoValidation of Experimentally Derived Data

Rid

Straßer²,

Siegl³

et al. 2013

ASSAY and Drug Development Technologies

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Steady improvements in proteomics present a bioinformatic challenge to retrieve, store, and process the accumulating and often redundant amount of information. In particular, a large-scale comparison and analysis of protein-protein interaction (PPI) data requires tools for data interpretation as well as validation. At this juncture, the Protein Interaction and Molecule Search (PRIMOS) platform represents a novel web portal that unifies six primary PPI databases (BIND, Biomolecular Interaction Network Database; DIP, Database of Interacting Proteins; HPRD, Human Protein Reference Database; IntAct; MINT, Molecular Interaction Database; and MIPS, Munich Information Center for Protein Sequences) into a single consistent repository, which currently includes more than 196,700 redundancy-removed PPIs. PRIMOS supports three advanced search strategies centering on disease-relevant PPIs, on inter- and intra-organismal crosstalk relations (e.g., pathogen-host interactions), and on highly connected protein nodes analysis ("hub" identification). The main novelties distinguishing PRIMOS from other secondary PPI databases are the reassessment of known PPIs, and the capacity to validate personal experimental data by our peer-reviewed, homology-based validation. This article focuses on definite PRIMOS use cases (presentation of embedded biological concepts, example applications) to demonstrate its broad functionality and practical value. PRIMOS is publicly available at http://primos.fh-hagenberg.at.

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“…Autoactivation of the transcription factor gives rise to the generation of 'false positives', perhaps the most common problem with the Y2H system. False positives are brought about by interactions of a non-biological origin, which occur independently of any physiologically relevant protein-protein interaction; that is those which only occur in the context of the screen, and would not normally occur under normal, non-Y2H, physiological conditions (Semple et al, 2002;Droit et al, 2005;Fields, 2005).…”

Section: Yeast Two Hybrid (Y2h)mentioning

confidence: 99%

Detection of Protein-Protein Interactions Using Protein-Fragment Complementation Assays (PCA)

Barnard¹,

McFerran²,

Nelson³

et al. 2007

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Protein-protein interactions play a central role in many cellular processes. Their characterisation is necessary in order to analyse these processes and for the functional identification of unknown proteins. Existing detection methods such as the yeast two-hybrid (Y2H) and tandem affinity purification (TAP) method provide a means to answer rapidly questions regarding protein-protein interactions, but have limitations which restrict their use to certain interaction networks; furthermore they provide little information regarding interaction localisation at the subcellular level. The development of protein-fragment complementation assays (PCA) employing a fluorescent reporter such as a member of the green fluorescent protein (GFP) family has led to a new method of interaction detection termed Bimolecular Fluorescent Complementation (BiFC). These assays have become important tools for understanding protein interactions and the development of whole genome interaction maps. BiFC assays have the advantages of very low background signal coupled with rapid detection of protein-protein interactions in vivo while also providing information regarding interaction compartmentalisation. Modified forms of the assay such as the use of combinations of spectral variants of GFP have allowed simultaneous visualisation of multiple competing interactions in vivo. Advantages and disadvantages of the method are discussed in the context of other fluorescence-based interaction monitoring techniques.

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The jury is out on 'guilt by association' trials

Cited by 13 publications

References 0 publications

A Protein Interaction Framework for Human mRNA Degradation

A Protein Interaction Framework for Human mRNA Degradation

PRIMOS: An Integrated Database of Reassessed Protein–Protein Interactions Providing Web-Based Access toIn SilicoValidation of Experimentally Derived Data

Detection of Protein-Protein Interactions Using Protein-Fragment Complementation Assays (PCA)

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