PPI layouts: BioJS components for the display of Protein-Protein Interactions

Salazar, Gustavo; Meintjes, Ayton; Mulder, Nicola

doi:10.12688/f1000research.3-50.v1

Cited by 9 publications

(3 citation statements)

References 18 publications

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“…The network in the web interface is drawn using the force-directed layout. The force-directed layout is useful for aggregating nodes according to their interaction ( 32 , 33 ). The layout enables easy identification of dense regions in a network, which may correspond to functional protein complexes ( 34 ).…”

Section: Methodsmentioning

confidence: 99%

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species

Kwon

Lee

Kim

et al. 2018

Nucleic Acids Research

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Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes during evolution can give us new insight into the evolution of functions. Although many algorithms, databases and websites have been developed to help the study of PPIs, most of them are limited to visualize the structure and features of PPIs in a chosen single species with limited functions in the visualization perspective. This leads to difficulties in the identification of different patterns of PPIs in different species and their functional consequences. To resolve these issues, we developed a web application, called INTER-Species Protein Interaction Analysis (INTERSPIA). Given a set of proteins of user's interest, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/.

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Section: Methodsmentioning

confidence: 99%

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species

Kwon

Lee

Kim

et al. 2018

Nucleic Acids Research

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“…BioJS is a community project to create a library of visual JavaScript components for biological sciences [ 11 ]. The main layout components of PINV are available in the BioJS registry [ 12 ], and were developed using D3 (Data-Driven Documents) [ 13 ], a JavaScript library for the manipulation of data and its visualization through web components.…”

Section: Methodsmentioning

confidence: 99%

A web-based protein interaction network visualizer

et al. 2014

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BackgroundInteraction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism’s processes. As of October 2013, Homo sapiens had over 170000 Protein-Protein interactions (PPI) registered in the Interologous Interaction Database, which is only one of the many public resources where protein interactions can be accessed. These numbers exemplify the volume of data that research on the topic has generated. Visualization of large data sets is a well known strategy to make sense of information, and protein interaction data is no exception. There are several tools that allow the exploration of this data, providing different methods to visualize protein network interactions. However, there is still no native web tool that allows this data to be explored interactively online.ResultsGiven the advances that web technologies have made recently it is time to bring these interactive views to the web to provide an easily accessible forum to visualize PPI. We have created a Web-based Protein Interaction Network Visualizer: PINV, an open source, native web application that facilitates the visualization of protein interactions (http://biosual.cbio.uct.ac.za/pinv.html). We developed PINV as a set of components that follow the protocol defined in BioJS and use the D3 library to create the graphic layouts. We demonstrate the use of PINV with multi-organism interaction networks for a predicted target from Mycobacterium tuberculosis, its interacting partners and its orthologs.ConclusionsThe resultant tool provides an attractive view of complex, fully interactive networks with components that allow the querying, filtering and manipulation of the visible subset. Moreover, as a web resource, PINV simplifies sharing and publishing, activities which are vital in today’s research collaborative environments. The source code is freely available for download at https://github.com/4ndr01d3/biosual.

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“…Among those components purposely built to render data visualisations for a particular a resource, we present KEGGViewer 5 , a component that visualises KEGG pathways; PsicquicGraph 6 , which visualises molecular interactions from PSICQUIC servers, and the InterMine List Analysis 7 and Table 8 components, which display statistical analyses and a dynamic result table, respectively, for InterMine-compatible data. Among components not designed for a particular resource, the collection includes FeatureViewer 9 , a component that lays out, maps and renders position-based annotations for protein sequences; HeatMapViewer 10 , which renders matrix-formatted data; treeWidget 11 , a component that visualises phylogenetic trees; a set of components to visualise protein-protein interaction networks 12 ; DAGViewer 13 , a directed acyclic graph viewer with facilities for rendering ontologies; Sequence 14 , a component for visualising sequences; wigExplorer 15 , which visualises wig format data; and DNAContentViewer 16 , which displays GC/AT content of a DNA sequence. The types of visualisation in this initial set of articles thus include network and directed acyclic graphs, a list, a table, generic features, a heat map, a phylogenetic tree and sequence-based objects.…”

Section: Commentarymentioning

confidence: 99%

The BioJS article collection of open source components for biological data visualisation

Corpas

2014

F1000Res

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Data-driven research has gained momentum in the life sciences. Visualisation of these data is essential for quick generation of hypotheses and their translation into useful knowledge. BioJS is a new proposed standard for JavaScript-based components to visualise biological data. BioJS is an open source community project that to date provides 39 different components contributed by a global community. Here, we present the BioJS F1000Research collection series. A total of 12 components and a project status article are published in bulk. This collection does not intend to be an all-encompassing, comprehensive source of BioJS articles, but an initial set; future submissions from BioJS contributors are welcome.

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PPI layouts: BioJS components for the display of Protein-Protein Interactions

Cited by 9 publications

References 18 publications

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species

A web-based protein interaction network visualizer

The BioJS article collection of open source components for biological data visualisation

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