InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

Abstract

BackgroundThe Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation.ResultsWe present InteGO2, a web tool that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks.ConclusionsInteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface. InteGO2 can be accessed via http://mlg.hit.edu.cn:8089/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2828-6) contains supplementary material, which is available to authorized users.

Accelerated Service Oriented Architecture Implementation of Deduplication Principle

“…Measurement of Scalability: This feature is to maintain WSCs with a large number of services and the services are prioritized by the scalability dimension. In this dimension, the GA-based approaches [10], and grade superior than IPbased services even if suboptimal results are accomplished. Complete GA-based functions advance the scalability by analysing with different params [11] such as the evolution policy, inhabitants and so on.…”

Erratum to: InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

“…After the publication of this supplement [1] the URL http://mlg.hit.edu.cn:8089/ceased to work and the new URL of https://mlg.hit.edu.cn/InteGO2 was created to replace it.…”

DisSetSim: An online system for calculating similarity between disease sets

“…Weight of edge is the functional similarity score. Then, disease-related miRNAs were prioritized using the network ranking algorithm named random walk with restart (RWR) [7]. The random walker starts on one or several seed nodes and then randomly transits to neighboring nodes considering the probabilities of the edges between the two nodes.…”

“…The similarity of pair-wise disease sets (SDS) has drawn more and more attention in identifying functional similarity of the disease-caused molecules [1], predicting potential relationships between diseases and molecules [2][3][4][5][6][7][8], and so on. In previous studies, Wang et al utilized the SDS to construct a human miRNA functional similarity network (MFSN) [1].…”

“…For comparing multiple aspects, the best measure is the PWBPA method, which is widely utilized in calculating similarity of DO and GO term sets [1,7,9,12].…”