View in EDS

NetSets.js: a JavaScript framework for compositional assessment and comparison of biological networks through Venn-integrated network diagrams.

Saved in:
Bibliographic Details
Title: NetSets.js: a JavaScript framework for compositional assessment and comparison of biological networks through Venn-integrated network diagrams.
Authors: Nagpal S; Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune 411 013, India., Kuntal BK; Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune 411 013, India., Mande SS; Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune 411 013, India.
Source: Bioinformatics (Oxford, England) [Bioinformatics] 2021 May 01; Vol. 37 (4), pp. 580-582.
Publication Type: Journal Article; Research Support, Non-U.S. Gov't
Language: English
Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s): Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms: Protein Interaction Maps* , Software*, Proteins/genetics
Abstract: Motivation: Venn diagrams are frequently used to compare composition of datasets (e.g. datasets containing list of proteins and genes). Network diagram constructed using such datasets are usually generated using 'list of edges', popularly known as edge-lists. An edge-list and the corresponding generated network are, however, composed of two elements, namely, edges (e.g. protein-protein interactions) and nodes (e.g. proteins). Researchers often use individual lists of edges and nodes to compare composition of biological networks using existing Venn diagram tools. However, specialized analysis workflows are required for comparison of nodes as well as edges. Apart from this, different tools or graph libraries are needed for visualizing any specific edges of interest (e.g. protein-protein interactions which are present across all networks or are shared between subset of networks or are exclusively present in a selected network). Further, these results are required to be exported in the form of publication worthy network diagram(s), particularly for small networks.
Results: We introduce a (server independent) JavaScript framework (called NetSets.js) that integrates popular Venn and network diagrams in a single application. A free to use intuitive web application (utilizing NetSets.js), specifically designed to perform both compositional comparisons (e.g. for identifying common/exclusive edges or nodes) and interactive user defined visualizations of network (for the identified common/exclusive interactions across multiple networks) using simple edge-lists is also presented. The tool also enables connection to Cytoscape desktop application using the Netsets-Cyapp. We demonstrate the utility of our tool using real world biological networks (microbiome, gene interaction, multiplex and protein-protein interaction networks).
Availabilityand Implementation: http://web.rniapps.net/netsets (freely available for academic use).
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Substance Nomenclature: 0 (Proteins)
Entry Date(s): Date Created: 20200818 Date Completed: 20210603 Latest Revision: 20210603
Update Code: 20260130
DOI: 10.1093/bioinformatics/btaa723
PMID: 32805035
Database: MEDLINE
Description
Abstract:Motivation: Venn diagrams are frequently used to compare composition of datasets (e.g. datasets containing list of proteins and genes). Network diagram constructed using such datasets are usually generated using 'list of edges', popularly known as edge-lists. An edge-list and the corresponding generated network are, however, composed of two elements, namely, edges (e.g. protein-protein interactions) and nodes (e.g. proteins). Researchers often use individual lists of edges and nodes to compare composition of biological networks using existing Venn diagram tools. However, specialized analysis workflows are required for comparison of nodes as well as edges. Apart from this, different tools or graph libraries are needed for visualizing any specific edges of interest (e.g. protein-protein interactions which are present across all networks or are shared between subset of networks or are exclusively present in a selected network). Further, these results are required to be exported in the form of publication worthy network diagram(s), particularly for small networks.<br />Results: We introduce a (server independent) JavaScript framework (called NetSets.js) that integrates popular Venn and network diagrams in a single application. A free to use intuitive web application (utilizing NetSets.js), specifically designed to perform both compositional comparisons (e.g. for identifying common/exclusive edges or nodes) and interactive user defined visualizations of network (for the identified common/exclusive interactions across multiple networks) using simple edge-lists is also presented. The tool also enables connection to Cytoscape desktop application using the Netsets-Cyapp. We demonstrate the utility of our tool using real world biological networks (microbiome, gene interaction, multiplex and protein-protein interaction networks).<br />Availabilityand Implementation: http://web.rniapps.net/netsets (freely available for academic use).<br />Supplementary Information: Supplementary data are available at Bioinformatics online.<br /> (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
ISSN:1367-4811
DOI:10.1093/bioinformatics/btaa723