Recurated protein interaction datasets

Salwiński, Łukasz; Licata, Luana; Winter, Andrew G.; Thorneycroft, David; Khadake, Jyoti; Céol, Arnaud; Aryamontri, Andrew Chatr; Oughtred, Rose; Livstone, Michael S.; Boucher, Lorrie; Botstein, David; Dolinski, Kara; Berardini, Tanya Z.; Huala, Eva; Tyers, Mike; Eisenberg, David; Cesareni, Gianni; Hermjakob, Henning

doi:10.1038/nmeth1209-860

Cited by 53 publications

(34 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the past years, genome-wide assays using two-hybrid and affinity purifications have identified many interactions now available in curated databases (19,20). However, because of methodological limitations, interactions between ER proteins remain under-represented, most likely because of their dependence on specific conditions for interaction, such as high calcium (21)(22)(23) and the oxidative environment of the ER (24 -26).…”

mentioning

confidence: 99%

An Interaction Map of Endoplasmic Reticulum Chaperones and Foldases

Jansen

Määttänen

Denisov

et al. 2012

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

Chaperones and foldases in the endoplasmic reticulum (ER) ensure correct protein folding. Extensive protein-protein interaction maps have defined the organization and function of many cellular complexes, but ER complexes are under-represented. Consequently, chaperone and foldase networks in the ER are largely uncharacterized. Using complementary ER-specific methods, we have mapped interactions between ER-lumenal chaperones and foldases and describe their organization in multiprotein complexes. We identify new functional chaperone modules, including interactions between protein-disulfide isomerases and peptidylprolyl cis-trans-isomerases. We have examined in detail a novel ERp72-cyclophilin B complex that enhances the rate of folding of immunoglobulin G. Deletion analysis and NMR reveal a conserved surface of cyclophilin B that interacts with polyacidic stretches of ERp72 and GRp94. Mutagenesis within this highly charged surface region abrogates interactions with its chaperone partners and reveals a new mechanism of ER protein-protein interaction. This ability of cyclophilin B to interact with different partners using the same molecular surface suggests that ER-chaperone/foldase partnerships may switch depending on the needs of different substrates, illustrating the flexibility of multichap-

show abstract

mentioning

confidence: 99%

An Interaction Map of Endoplasmic Reticulum Chaperones and Foldases

Jansen

Määttänen

Denisov

et al. 2012

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

show abstract

“…A Correspondence 71 by members of the International Molecular Exchange Consortium (IMEx), while accepting many of our points, objected to our recuration exercise to assess quality, finding our criteria "subjective." We argue that the criteria were commonsensical and essentially capture how these databases are often described.…”

Section: Addenda Corrigenda and Erratamentioning

confidence: 99%

“…Almost 90% of interactions, and 95% of the problematic curation units, came from non-IMEX databases (HPRD 22 and BIND 17 ). We had been requested to omit this information originally, but for IMEX databases there is minimal difference in error rates between our recuration and that of Salwinski et al 71 . A download discrepancy, which IntAct has now mended so that it cannot recur, necessitated the recuration of the errors for the Arabidopsis curation (Supplementary Table 4 in our original Perspective).…”

Section: Addenda Corrigenda and Erratamentioning

confidence: 99%

“…In papers in Trends in Biochemical Sciences 44,45,51 the authors argued over a distressing lack of reproducibility of curated interactions and contended that "protein interactions reported in the literature and curated in interaction databases might not occur as presented." Other reports have questioned the presumed perfection of curated PPIs 23,29,43,74 , even one report by several authors of Salwinski et al 71 : "a comparison of publications curated by both MINT and IntAct between 2003 and 2005 revealed that the two databases annotated exactly the same interaction pairs in only 6 out of 52 publications" 75 . BioGRID now grants that provisions are not made for quality assessment in curation: "We make no judgement calls on the methods or even, within reason, the quality of the data themselves" 76 .…”

Section: Addenda Corrigenda and Erratamentioning

confidence: 99%

See 1 more Smart Citation

Addendum: Literature-curated protein interaction datasets

Cusick¹,

Yu²,

Smolyar³

et al. 2009

Nat Methods

View full text Add to dashboard Cite

934 | VOL.6 NO.12 | DECEMBER | nature methods addenda, corrigenda and errataWe assessed literature-curated protein-protein interaction (PPI) datasets for the parameters of completeness, coverage and quality by several means, concluding that such datasets might be "possibly of lower quality than commonly assumed." A Correspondence 71 by members of the International Molecular Exchange Consortium (IMEx), while accepting many of our points, objected to our recuration exercise to assess quality, finding our criteria "subjective." We argue that the criteria were commonsensical and essentially capture how these databases are often described.A wide swath of the scientific community, from computer scientists and engineers to physicists, systems biologists and molecular biologists, use literature-curated datasets as 'gold-standard' positive controls with the tacit understanding that this information is nearly perfect. Whether user impressions were formed from statements made by database authors [18][19][20][21] or not, belief that database entries accurately correspond to high-quality, direct physical interactions is widespread 6,72 . The standards we used to assess quality are generally accepted by the IMEx members, but one that remains problematic is the definition of binary interactions. A meaningful fraction of database users is under the impression that 'binary interaction' means direct pairwise PPIs, and that is the definition we tried to apply. The definition that the IMEx databases apply is that of 'binary representation' , meaning any pairwise association between two entities, direct or indirect. Although technically correct from an informatics viewpoint, binary representation likely does not accurately reflect biophysical reality. To better match user expectations, one IMEx database has adjusted their website presentation to allow users to filter 'spoke expanded co-complexes' from binary interactions, although all reported interactions are initially classified as 'binary' .Another widespread perception is that curated databases contain predominantly low-throughput interactions, whereas the reality is that curated databases have a substantial portion of interactions derived from high-throughput experiments ( Fig. 2 in our Perspective). The point is not whether high-throughput interaction experiments are of worse or better quality than low-throughput experiments, but that greater transparency should be provided so that users can filter the data according to their needs.As a result of applying the criteria that we did, based on the observations above, the error rates we reported reflected not only errors in curation but also how well the underlying data meet the standards set forth. The details for the yeast, human and plant recurations are available in the Supplementary Note.Our efforts are aimed at alerting the scientific community that literature-curated interactions may need further scrutiny or classification to qualify as a 'gold standard' for users who are specifically interested in direct pairwise PPIs. Clos...

show abstract

“…This is dependent on curation accuracy, which has been a topic of debate recently. Two recent studies found very different levels of curation accuracy within the data sets sampled using different approaches (Cusick et al, 2009a;Salwinski et al, 2009 (Cusick et al, 2009b;Salwinski et al, 2009). The conclusions that can be drawn from this debate are that expert appraisal of repositories' veracity is central to quality assurance and that all participants in the production, capture, storage, and dissemination of the data can take steps to lower error rates.…”

Section: Composition Of the Intact And Other Arabidopsis Interaction mentioning

confidence: 99%

Mapping Plant Interactomes Using Literature Curated and Predicted Protein–Protein Interaction Data Sets

et al. 2010

Self Cite

View full text Add to dashboard Cite

Most cellular processes are enabled by cohorts of interacting proteins that form dynamic networks within the plant proteome. The study of these networks can provide insight into protein function and provide new avenues for research. This article informs the plant science community of the currently available sources of protein interaction data and discusses how they can be useful to researchers. Using our recently curated IntAct Arabidopsis thaliana protein-protein interaction data set as an example, we discuss potentials and limitations of the plant interactomes generated to date. In addition, we present our efforts to add value to the interaction data by using them to seed a proteome-wide map of predicted protein subcellular locations.For well over two decades, plant scientists have studied protein interactions within plants using many different and evolving approaches. Their findings are represented by a large and growing corpus of peer-reviewed literature reflecting the increasing activity in this area of plant proteomic research. More recently, a number of predicted interactomes have been reported in plants and, while these predictions remain largely untested, they could act as a useful guide for future research. These studies have allowed researchers to better understand the function of protein complexes and to refine our understanding of protein function within the cell (Uhrig, 2006;Morsy et al., 2008). The extraction of protein interaction data from the literature and its standardized deposition and representation within publicly available databases remains a challenging task. Aggregating the data in databases allows researchers to leverage visualization, data mining, and integrative approaches to produce new insights that would be unachievable when the data are dispersed within largely inaccessible formats (Rodriguez et al., 2009).Currently, there are three databases that act as repositories of plant protein interaction data. These are IntAct

show abstract

Recurated protein interaction datasets

Cited by 53 publications

References 8 publications

An Interaction Map of Endoplasmic Reticulum Chaperones and Foldases

An Interaction Map of Endoplasmic Reticulum Chaperones and Foldases

Addendum: Literature-curated protein interaction datasets

Mapping Plant Interactomes Using Literature Curated and Predicted Protein–Protein Interaction Data Sets

Contact Info

Product

Resources

About