Fabiano de Oliveira Poswar1, Lucyana Conceição Farias2, Carlos Alberto de Carvalho Fraga1, Wilson Bambirra3, Manoel Brito-Júnior1, Manoel Damião Sousa-Neto4, Sérgio Henrique Souza Santos5, Alfredo Maurício Batista de Paula1, Marcos Flávio Silveira Vasconcelos D'Angelo6, André Luiz Sena Guimarães7. 1. Department of Dentistry, Universidade Estadual de Montes Claros, Minas Gerais, Brazil. 2. Department of Physiopathology, Universidade Estadual de Montes Claros, Minas Gerais, Brazil. 3. Department of Restorative Dentistry, Faculty of Dentistry, Universidade Federal de Minas Gerais, Minas Gerais, Brazil. 4. Department of Restorative Dentistry, Faculty of Dentistry, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil. 5. Department of Physiopathology, Universidade Estadual de Montes Claros, Minas Gerais, Brazil; Department of Computer Science, Universidade Estadual de Montes Claros, Minas Gerais, Brazil; 6. Department of Computer Science, Universidade Estadual de Montes Claros, Minas Gerais, Brazil; 7. Department of Dentistry, Universidade Estadual de Montes Claros, Minas Gerais, Brazil. Electronic address: andreluizguimaraes@gmail.com.
Abstract
INTRODUCTION: Bioinformatics has emerged as an important tool to analyze the large amount of data generated by research in different diseases. In this study, gene expression for radicular cysts (RCs) and periapical granulomas (PGs) was characterized based on a leader gene approach. METHODS: A validated bioinformatics algorithm was applied to identify leader genes for RCs and PGs. Genes related to RCs and PGs were first identified in PubMed, GenBank, GeneAtlas, and GeneCards databases. The Web-available STRING software (The European Molecular Biology Laboratory [EMBL], Heidelberg, Baden-Württemberg, Germany) was used in order to build the interaction map among the identified genes by a significance score named weighted number of links. Based on the weighted number of links, genes were clustered using k-means. The genes in the highest cluster were considered leader genes. Multilayer perceptron neural network analysis was used as a complementary supplement for gene classification. RESULTS: For RCs, the suggested leader genes were TP53 and EP300, whereas PGs were associated with IL2RG, CCL2, CCL4, CCL5, CCR1, CCR3, and CCR5 genes. CONCLUSIONS: Our data revealed different gene expression for RCs and PGs, suggesting that not only the inflammatory nature but also other biological processes might differentiate RCs and PGs.
INTRODUCTION: Bioinformatics has emerged as an important tool to analyze the large amount of data generated by research in different diseases. In this study, gene expression for radicular cysts (RCs) and periapical granulomas (PGs) was characterized based on a leader gene approach. METHODS: A validated bioinformatics algorithm was applied to identify leader genes for RCs and PGs. Genes related to RCs and PGs were first identified in PubMed, GenBank, GeneAtlas, and GeneCards databases. The Web-available STRING software (The European Molecular Biology Laboratory [EMBL], Heidelberg, Baden-Württemberg, Germany) was used in order to build the interaction map among the identified genes by a significance score named weighted number of links. Based on the weighted number of links, genes were clustered using k-means. The genes in the highest cluster were considered leader genes. Multilayer perceptron neural network analysis was used as a complementary supplement for gene classification. RESULTS: For RCs, the suggested leader genes were TP53 and EP300, whereas PGs were associated with IL2RG, CCL2, CCL4, CCL5, CCR1, CCR3, and CCR5 genes. CONCLUSIONS: Our data revealed different gene expression for RCs and PGs, suggesting that not only the inflammatory nature but also other biological processes might differentiate RCs and PGs.
Authors: Eliane Macedo Sobrinho Santos; Hércules Otacílio Santos; Ivoneth Dos Santos Dias; Sérgio Henrique Santos; Alfredo Maurício Batista de Paula; John David Feltenberger; André Luiz Sena Guimarães; Lucyana Conceição Farias Journal: Int J Mol Cell Med Date: 2016-12-06
Authors: Talita Antunes Guimarães; Lucyana Conceição Farias; Eliane Sobrinho Santos; Carlos Alberto de Carvalho Fraga; Lissur Azevedo Orsini; Leandro de Freitas Teles; John David Feltenberger; Sabrin Ferreira de Jesus; Marcela Gonçalves de Souza; Sérgio Henrique Sousa Santos; Alfredo Maurício Batista de Paula; Ricardo Santiago Gomez; André Luiz Sena Guimarães Journal: Oncotarget Date: 2016-08-23