The minimum information required for reporting a molecular interaction experiment (MIMIx)

Orchard, Sandra; Salwiński, Łukasz; Kerrien, Samuel; Montecchi-Palazzi, Luisa; Oesterheld, Matthias; Stümpflen, Volker; Céol, Arnaud; Chatr‐aryamontri, Andrew; Armstrong, J. T.; Woollard, Peter; Salama, John J.; Moore, Susan; Wojcik, Jérôme; Bader, Gary D.; Vidal, Marc; Cusick, Michael E.; Gerstein, Mark; Gavin, Anne‐Claude; Superti‐Furga, Giulio; Greenblatt, Jack; Bader, Joel S.; Uetz, Peter; Tyers, Mike; Legrain, Pierre; Fields, Stan; Mulder, Nicola; Gilson, Michael K.; Niepmann, Michael; Burgoon, Lyle D.; Rivas, Javier De Las; Prieto, Carlos; Perreau, Victoria M.; Hogue, Christopher W. V.; Mewes, Hans‐Werner; Apweiler, Rolf; Xenarios, Ioannis; Eisenberg, David; Cesareni, Gianni; Hermjakob, Henning

doi:10.1038/nbt1324

Cited by 261 publications

(165 citation statements)

References 22 publications

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“…To establish a standardized system to analyze these ISTs, we developed pISTil, a bioinformatics pipeline combined to a user-friendly Web interface (see Note 30) (18). The pISTil system is highly flexible and allows (a) systematic and fast assignation of ISTs to a unique protein accession number; (b) annotation of "in-frame" or not-in-frame ISTs; (c) manual checking and visualization of annotated ISTs through a userfriendly Web interface; and (d) export of ppi in multiple formats, such as MIMIx standard format (19).…”

Section: Grow Each Yeast Bait Colony Overnight In 2 ML Sd-w Under Agimentioning

confidence: 99%

Virus–Human Cell Interactomes

Tafforeau¹,

Rabourdin–Combe²,

Lotteau³

2011

Methods in Molecular Biology

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Using global approaches and high-throughput technologies in virology brings a new vision of the infections physiology and allows the identification of cellular factors, mandatory for viral life cycle, that could be targeted by original therapeutic agents. It opens perspectives for the treatment of viral infections by acting on cellular pathways that the virus must use for its own replication. Combining these new molecules with classical antiviral drugs and immunomodulators diversifies and enlarges the antiviral arsenal and contributes to fight drug resistance.Our laboratory and others are constructing virus-human interactomes to propose a comprehensive analysis of viral infection at the cellular level. Studying these infection maps, where the viral infection can be visualized as perturbation of the human protein-protein interaction network, and identifying the biological functions that are impaired by these perturbations may lead to discovery of new therapeutic targets. These virus-human interaction maps are constructed in a stringent yeast two-hybrid system by screening human cDNA libraries with viral proteins as bait and integrating interactions mined from literature and public databases. Key words:Yeast two-hybrid screen, Mating, Yeast two-hybrid array, Protein-protein interactionThe rapidly growing knowledge of protein-protein interaction networks (interactomes) for model organisms and human provides a network-based model to understand molecular and cellular biology. Recently, virus-host relationships also began to be studied at the proteome level by identifying interactions between viral and host-cell proteins (1-5), as reviewed in ref. 6. These virus-host interactomes compose a repertoire of interactions between viral and human proteins that can be analyzed in a network approach. By this mean, viral infections can be viewed as the expression of new constraints imposed by the virus on the cellular interactome.

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Section: Grow Each Yeast Bait Colony Overnight In 2 ML Sd-w Under Agimentioning

confidence: 99%

Virus–Human Cell Interactomes

Tafforeau¹,

Rabourdin–Combe²,

Lotteau³

2011

Methods in Molecular Biology

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“…Options propose to select interactions stored within 1 to 31 databases gathered by the PSICQUIC website [17]. User can select the databases depending on the type of interactions (PPi, Nucleic acid-Protein interaction (NPi), and Smallmolecule-Protein interaction (SPi)) and the data (curated, predicted, curated according to the IMEx project [26] or the MIMIx curation [27] In addition to the web interface, ProteINSIDE is composed of a database and a workflow.…”

Section: Proteinside's Featuresmentioning

confidence: 99%

“…The basic analysis identifies PPi within the uploaded dataset (core network) using the preselected databases IntAct, UniProt, and BioGrid. These PPi databases were chosen as a default option because there are daily updated and reviewed by curators as well as by the curation processes of the IMEx project (that ensures reliable interactions data using experts and curation rules shared between many interaction databases [26]) or MIMIx (a guideline of the minimum information required for reporting a molecular interaction experiment, thus advising the user on how to use the interaction data [27]). Moreover, BioGrid is the biggest PPi database that has its own curation workflow (more than 740000 curated PPi) and is not a partner of IMex curation program.…”

Section: Analyses and Datamentioning

confidence: 99%

Protein Function Easily Investigated by Genomics Data Mining Using the ProteINSIDE Online Tool

Kaspric¹,

Reichstadt²,

Picard³

et al. 2015

Genomics Comput Biol

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Nowadays, genomic and proteomic studies produce vast amounts of data. To get the biological meaning of these data and to generate testable new hypothesis, scientists must use several tools often not designed for ruminant studies. Here we present ProteINSIDE: an online tool to analyse lists of protein or gene identifiers from well-annotated species (human, rat, and mouse) and ruminants (cow, sheep, and goat). The aims of ProteINSIDE modules are to gather biological information stores in well-updated public databases, to proceed to annotations according to the Gene Ontology consortium, to predict potentially secreted proteins, and to search for proteins interactions. ProteINSIDE provides results from several software and databases in a single query. From a list of identifiers, ProteINSIDE uses orthologs or homologs to extend analyses and biological information retrieval. As a tutorial, we presented how to launch, to recover, to view, and to interpret the results provided by the two types of analysis available with ProteINSIDE (basic and custom analyses). ProteINSIDE is freely available using an internet browser at www.proteinside.org. The results of this article are provided on the home page of ProteINSIDE website as the example of an analysis result.

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“…[57], The Database of Interacting Proteins (DIP) [58], IntAct [59,60], Molecular INTeraction database (MINT) [61], and BioGRID [62,63]. Furthermore, HUPO, through the HUPO Proteomics Standard initiative, has recently proposed standards required for the submission of interaction datasets [64]. These repositories provide access to the interaction datasets and some levels of annotation.…”

Section: Immunopurification Protocolsmentioning

confidence: 99%

Mapping the human protein interactome

Figeys

2008

Cell Res

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Interactions are the essence of all biomolecules because they cannot fulfill their roles without interacting with other molecules. Hence, mapping the interactions of biomolecules can be useful for understanding their roles and functions. Furthermore, the development of molecular based systems biology requires an understanding of the biomolecular interactions. In recent years, the mapping of protein-protein interactions in different species has been reported, but few reports have focused on the large-scale mapping of protein-protein interactions in human. Here, we review the developments in protein interaction mapping and we discuss issues and strategies for the mapping of the human protein interactome. The latest craze in science is systems biology. Scientists in different scientific fields, however, define and view "systems biology" in different ways. Systems biology, for example, can mean mathematical modeling of a system for accurate predictions of the behavior of the system. It can also mean the systematic application of different highthroughput approaches to gather information on the system and to combine different information spaces for a more comprehensible view of the biology at hand. To date, the best modeling and predictions have been on systems for which good biological information is available [1]. Hence, gathering information on the system is required to develop predictive models. Genomics has been the primary source of large-scale information on systems through genome sequencing, large-scale SNPs analyses, and gene expression studies. KeywordsThe success of genomics has snow-balled into other areas, such as the large-scale data gathering at the protein level (proteomics). One of the achievements of proteomics is the mapping of protein interactions (interactome; the ensemble of the protein interactions related to a proteome or a genome). We have seen a growing number of large-scale studies of the interactome (or part of) for different species including yeast [2][3][4][5][6][7] Should the human protein interactome be mapped?The first question can be easily answered and is reminiscent of early discussions about sequencing the human genome. Many scientists were doubtful that sequencing the human genome would be worth the effort. It is now clear that today's research in human diseases and biological processes benefits from the human genome project. We already have a glimpse of the potential outcomes of mapping the human interactome by looking at the yeast interactome. The importance of mapping the yeast interactome can be measured in different ways; however, the number of references to the original papers by Fields [22] (over 3 000 citations) for interaction mapping by Y2H; and Ho [4] (over 1 300 citations) and Gavin [6] (over 1 400 citations) for protein interaction mapping by mass spectrometry clearly npg Cell Research (2008) 18:716-724.

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The minimum information required for reporting a molecular interaction experiment (MIMIx)

Cited by 261 publications

References 22 publications

Virus–Human Cell Interactomes

Virus–Human Cell Interactomes

Protein Function Easily Investigated by Genomics Data Mining Using the ProteINSIDE Online Tool

Mapping the human protein interactome

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