DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks

Renaud, Yoan; Baillif, Alexandre; Perez, Jean-Baptiste; Agier, Marie; Nguifo, Engelbert Mephu; Mirouse, Vincent

doi:10.1093/nar/gks434

Cited by 5 publications

(5 citation statements)

References 21 publications

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“… Interaction networks of CASK-associated proteins . Interaction networks were detected using DroPNet (Renaud et al, 2012 ), a web-based interface for building networks. Proteins found in each cell type were loaded into DroPNet and searched against Drosophila , Yeast, Human, and Worm protein interaction databases.…”

Section: Resultsmentioning

confidence: 99%

“…To determine functional groupings of interactors, the CG numbers of genes for which peptides were found were identified from FLYBASE and used as input in DroPNet (Renaud et al, 2012 ), a web-based interface for building networks ( https://dropnet.gred-clermont.fr/DroPNet_project/index.faces ). Networks were created inclusive of all the filters.…”

Section: Methodsmentioning

confidence: 99%

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Neuron-specific protein interactions of Drosophila CASK-Î² are revealed by mass spectrometry

Mukherjee¹,

Slawson²,

Christmann³

et al. 2014

Front. Mol. Neurosci.

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Modular scaffolding proteins are designed to have multiple interactors. CASK, a member of the membrane-associated guanylate kinase (MAGUK) superfamily, has been shown to have roles in many tissues, including neurons and epithelia. It is likely that the set of proteins it interacts with is different in each of these diverse tissues. In this study we asked if within the Drosophila central nervous system, there were neuron-specific sets of CASK-interacting proteins. A YFP-tagged CASK-β transgene was expressed in genetically defined subsets of neurons in the Drosophila brain known to be important for CASK function, and proteins present in an anti-GFP immunoprecipitation were identified by mass spectrometry. Each subset of neurons had a distinct set of interacting proteins, suggesting that CASK participates in multiple protein networks and that these networks may be different in different neuronal circuits. One common set of proteins was associated with mitochondria, and we show here that endogenous CASK-β co-purifies with mitochondria. We also determined CASK-β posttranslational modifications for one cell type, supporting the idea that this technique can be used to assess cell- and circuit-specific protein modifications as well as protein interaction networks.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Neuron-specific protein interactions of Drosophila CASK-Î² are revealed by mass spectrometry

Mukherjee¹,

Slawson²,

Christmann³

et al. 2014

Front. Mol. Neurosci.

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“…Indeed, many tools are dedicated to only one species such as BioMyn for the Human [9] or DroPNet for the Drosophila [7]). Moreover, many tools are dedicated to diseases studies such as NetPath [13] and ToppGene [12].…”

Section: Discussionmentioning

confidence: 99%

“…Such bioinformatic data processing has to proceed to data gathering and database searching in order to produce a functional interpretation of large datasets. For this purpose, workflows integrating several bioinformatics analyses are now available [5][6][7][8] and were developed to mine dataset from specific species (BioMyn [9] for human, DroPNet [7] for Drosophila, TAIR [10] for Arabidopsis thaliana, EcoCyc [11] for Escherichia coli …) or to identify candidate genes related to diseases as ToppGene [12] or NetPath [13]. The few workflows currently used for the bioinformatics data processing of ruminant datasets are multispecies.…”

Section: Introductionmentioning

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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“…Network alignment is the process of globally comparing two networks, identifying regions of similarity and to detect subnetworks that are conserved across species. Analyzing PPI networks, has been very effective in tackling many problems such as understanding the genetic factors that impact various diseases [5], drug discovery [6], predicting protein functions [7,8,9,10], identifying functional modules [11], and understanding the phylogeny from these data.…”

Section: Introductionmentioning

confidence: 99%

A Novel Computational Approach for Global Alignment for Multiple Biological Networks

Djeddi

Yahia

Nguifo

2018

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Due to the rapid progress of biological networks for modeling biological systems, a lot of biomolecular networks have been producing more and more protein-protein interaction (PPI) data. Analyzing protein-protein interaction (PPI) networks aims to find regions of topological and functional (dis)similarities between molecular networks of different species. The study of PPI networks has the potential to teach us as much about life process and diseases at the molecular level. Although few methods have been developed for multiple PPI network alignment and thus, new network alignment methods are of a compelling need. In this paper, we propose a novel algorithm for a global alignment of multiple protein-protein interaction (PPI) networks called MAPPIN. The latter relies on information available for the proteins in the networks, such as sequence, function and network topology. Our algorithm is perfectly designed to exploit current multi-core CPU architectures, and has been extensively tested on a real data (eight species). Our experimental results show that MAPPIN significantly outperforms NetCoffee in terms of coverage. Nevertheless, MAPPIN is handicapped by the time required to load the gene annotation file. An extensive comparison versus the pioneering PPI methods also show that MAPPIN is often efficient in terms of coverage, mean entropy or mean normalized.

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DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks

Cited by 5 publications

References 21 publications

Neuron-specific protein interactions of Drosophila CASK-Î² are revealed by mass spectrometry

Neuron-specific protein interactions of Drosophila CASK-Î² are revealed by mass spectrometry

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

A Novel Computational Approach for Global Alignment for Multiple Biological Networks

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