Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases
Objective It is increasingly common to find patients affected by a combination of type 2 diabetes mellitus (T2DM), dyslipidemia (DLP) and periodontitis (PD), which are chronic inflammatory diseases. More studies able to capture unknown relationships among these diseases will contribute to raise biol...
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doaj-01dce2114d8b4dfd94180e7902cd13a12020-11-25T03:43:35ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-011510Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseasesRosana VeronezeSâmia Cruz Tfaile CorbiBárbara Roque da SilvaCristiane de S. RochaCláudia V. Maurer-MorelliSilvana Regina Perez OrricoJoni A. CirelliFernando J. Von ZubenRaquel Mantuaneli Scarel-CaminagaPaolo MagniObjective It is increasingly common to find patients affected by a combination of type 2 diabetes mellitus (T2DM), dyslipidemia (DLP) and periodontitis (PD), which are chronic inflammatory diseases. More studies able to capture unknown relationships among these diseases will contribute to raise biological and clinical evidence. The aim of this study was to apply association rule mining (ARM) to discover whether there are consistent patterns of clinical features (CFs) and differentially expressed genes (DEGs) relevant to these diseases. We intend to reinforce the evidence of the T2DM-DLP-PD-interplay and demonstrate the ARM ability to provide new insights into multivariate pattern discovery. Methods We utilized 29 clinical glycemic, lipid and periodontal parameters from 143 patients divided into five groups based upon diabetic, dyslipidemic and periodontal conditions (including a healthy-control group). At least 5 patients from each group were selected to assess the transcriptome by microarray. ARM was utilized to assess relevant association rules considering: (i) only CFs; and (ii) CFs+DEGs, such that the identified DEGs, specific to each group of patients, were submitted to gene expression validation by quantitative polymerase chain reaction (qPCR). Results We obtained 78 CF-rules and 161 CF+DEG-rules. Based on their clinical significance, Periodontists and Geneticist experts selected 11 CF-rules, and 5 CF+DEG-rules. From the five DEGs prospected by the rules, four of them were validated by qPCR as significantly different from the control group; and two of them validated the previous microarray findings. Conclusions ARM was a powerful data analysis technique to identify multivariate patterns involving clinical and molecular profiles of patients affected by specific pathological panels. ARM proved to be an effective mining approach to analyze gene expression with the advantage of including patient’s CFs. A combination of CFs and DEGs might be employed in modeling the patient’s chance to develop complex diseases, such as those studied here.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531780/?tool=EBI |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Rosana Veroneze Sâmia Cruz Tfaile Corbi Bárbara Roque da Silva Cristiane de S. Rocha Cláudia V. Maurer-Morelli Silvana Regina Perez Orrico Joni A. Cirelli Fernando J. Von Zuben Raquel Mantuaneli Scarel-Caminaga Paolo Magni |
spellingShingle |
Rosana Veroneze Sâmia Cruz Tfaile Corbi Bárbara Roque da Silva Cristiane de S. Rocha Cláudia V. Maurer-Morelli Silvana Regina Perez Orrico Joni A. Cirelli Fernando J. Von Zuben Raquel Mantuaneli Scarel-Caminaga Paolo Magni Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases PLoS ONE |
author_facet |
Rosana Veroneze Sâmia Cruz Tfaile Corbi Bárbara Roque da Silva Cristiane de S. Rocha Cláudia V. Maurer-Morelli Silvana Regina Perez Orrico Joni A. Cirelli Fernando J. Von Zuben Raquel Mantuaneli Scarel-Caminaga Paolo Magni |
author_sort |
Rosana Veroneze |
title |
Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases |
title_short |
Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases |
title_full |
Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases |
title_fullStr |
Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases |
title_full_unstemmed |
Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases |
title_sort |
using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2020-01-01 |
description |
Objective It is increasingly common to find patients affected by a combination of type 2 diabetes mellitus (T2DM), dyslipidemia (DLP) and periodontitis (PD), which are chronic inflammatory diseases. More studies able to capture unknown relationships among these diseases will contribute to raise biological and clinical evidence. The aim of this study was to apply association rule mining (ARM) to discover whether there are consistent patterns of clinical features (CFs) and differentially expressed genes (DEGs) relevant to these diseases. We intend to reinforce the evidence of the T2DM-DLP-PD-interplay and demonstrate the ARM ability to provide new insights into multivariate pattern discovery. Methods We utilized 29 clinical glycemic, lipid and periodontal parameters from 143 patients divided into five groups based upon diabetic, dyslipidemic and periodontal conditions (including a healthy-control group). At least 5 patients from each group were selected to assess the transcriptome by microarray. ARM was utilized to assess relevant association rules considering: (i) only CFs; and (ii) CFs+DEGs, such that the identified DEGs, specific to each group of patients, were submitted to gene expression validation by quantitative polymerase chain reaction (qPCR). Results We obtained 78 CF-rules and 161 CF+DEG-rules. Based on their clinical significance, Periodontists and Geneticist experts selected 11 CF-rules, and 5 CF+DEG-rules. From the five DEGs prospected by the rules, four of them were validated by qPCR as significantly different from the control group; and two of them validated the previous microarray findings. Conclusions ARM was a powerful data analysis technique to identify multivariate patterns involving clinical and molecular profiles of patients affected by specific pathological panels. ARM proved to be an effective mining approach to analyze gene expression with the advantage of including patient’s CFs. A combination of CFs and DEGs might be employed in modeling the patient’s chance to develop complex diseases, such as those studied here. |
url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531780/?tool=EBI |
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