Abstract
ABSTRACTObjective: Burkitt's lymphoma (BL) is a highly aggressive malignant lymphoma, its molecular biological mechanism has not been fully investigated. The construction of protein-protein interaction (PPI) networks and the identification of complexes through a cluster analysis are important research directions in the post-genome era. However, different cluster analysis algorithms have their own characteristics, and a single analysis has some limitations. In this study, we obtained the target and pathway information of BL using different clustering analyses.Material and Methods: First, we obtained 50 BL genes by screening the Online Mendelian Inheritance in Man (OMIM) database; their related genes were further extracted from the literature. The PPI network was constructed with the Search Tool for Retrieval of Interacting Genes/Proteins (STRING). Afterward, the interaction data were input in Cytoscape3.4.0 software and related plug-ins were used to implement topology analysis and clustering analysis. Functional analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to characterize the biological importance of the clusters.Results: We constructed a PPI network consisting of 459 nodes (proteins) and 1399 sides (interactions), 12 genes and 8 signaling pathways were found to be closely related to BL.Conclusion: In this study, the use of combined algorithms to analyse gene interactions provides a new perspective for network-based analysis. The results of this study reveal new insights into the molecular mechanisms underlying BL, which may be novel therapeutic targets for disease management and may provide a bioinformatic basis for the further understanding of BL.
Highlights
The protein interaction was read into Cytoscape 3.4.0, which allows the network to be integrated into any type of attribute data and implement topology analysis [9]
The first five enrichment pathways of each molecular complex are listed in the table, but we took all meaningful data for analysis
Nanda Kumar Yellapu, etc., through the analysis of the protein-protein interaction (PPI) network found that PAK1 is an important target gene of breast cancer [15]; Ma [16] used microarray and system biology methods to describe the genetic background of cold syndrome in the TCM system
Summary
Searching for BL-related genesBL-related genes were extracted from the Online Mendelian Inheritance in Man (OMIM) database, using the C. Sixty-eight BL-related genes were identified (up to 2016-07-26); By reading the related articles one by one, miscellaneous data were screened out. PPI network construction and topology attribute analysis. The Search Tool for the Retrieval of Interacting Genes/ Protein (STRING) database was used to retrieve the predicted interactions for the identified genes and allows visualizing complex networks [8]. Version 10.0 of STRING, which contains information on approximately 9.6 million proteins from more than 2000 organisms is a biological database and web resource of known and predicted PPIs. We set the required interaction score at >0.4 as the threshold used for analysis. The protein interaction was read into Cytoscape 3.4.0 (http://cytoscape.org/), which allows the network to be integrated into any type of attribute data and implement topology analysis [9]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
