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Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm

OBJECTIVE: Thyroid Cancer (TC) is the most frequent endocrine malignancy neoplasm. It is the sixth cause of cancer in women worldwide. The treatment process could be expedited by identifying the controlling molecular mechanisms at the early and late stages, which can contribute to the acceleration o...

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Autores principales: Hosseiniyan Khatibi, Seyed Mahdi, Zununi Vahed, Sepideh, Homaei Rad, Hamed, Emdadi, Manijeh, Akbarpour, Zahra, Teshnehlab, Mohammad, Pirmoradi, Saeed, Alizadeh, Effat
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621943/
https://www.ncbi.nlm.nih.gov/pubmed/37917782
http://dx.doi.org/10.1371/journal.pone.0293335
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author Hosseiniyan Khatibi, Seyed Mahdi
Zununi Vahed, Sepideh
Homaei Rad, Hamed
Emdadi, Manijeh
Akbarpour, Zahra
Teshnehlab, Mohammad
Pirmoradi, Saeed
Alizadeh, Effat
author_facet Hosseiniyan Khatibi, Seyed Mahdi
Zununi Vahed, Sepideh
Homaei Rad, Hamed
Emdadi, Manijeh
Akbarpour, Zahra
Teshnehlab, Mohammad
Pirmoradi, Saeed
Alizadeh, Effat
author_sort Hosseiniyan Khatibi, Seyed Mahdi
collection PubMed
description OBJECTIVE: Thyroid Cancer (TC) is the most frequent endocrine malignancy neoplasm. It is the sixth cause of cancer in women worldwide. The treatment process could be expedited by identifying the controlling molecular mechanisms at the early and late stages, which can contribute to the acceleration of treatment schemes and the improvement of patient survival outcomes. In this work, we study the significant mRNAs through Machine Learning Algorithms in both the early and late stages of Papillary Thyroid Cancer (PTC). METHOD: During the course of our study, we investigated various methods and techniques to obtain suitable results. The sequence of procedures we followed included organizing data, using nested cross-validation, data cleaning, and normalization at the initial stage. Next, to apply feature selection, a t-test and binary Non-Dominated Sorting Genetic Algorithm II (NSGAII) were chosen to be employed. Later on, during the analysis stage, the discriminative power of the selected features was evaluated using machine learning and deep learning algorithms. Finally, we considered the selected features and utilized Association Rule Mining algorithm to identify the most important ones for improving the decoding of dominant molecular mechanisms in PTC through its early and late stages. RESULT: The SVM classifier was able to distinguish between early and late-stage categories with an accuracy of 83.5% and an AUC of 0.78 based on the identified mRNAs. The most significant genes associated with the early and late stages of PTC were identified as (e.g., ZNF518B, DTD2, CCAR1) and (e.g., lnc-DNAJB6-7:7, RP11-484D2.3, MSL3P1), respectively. CONCLUSION: Current study reveals a clear picture of the potential candidate genes that could play a major role not only in the early stage, but also throughout the late one. Hence, the findings could be of help to identify therapeutic targets for more effective PTC drug developments.
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spelling pubmed-106219432023-11-03 Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm Hosseiniyan Khatibi, Seyed Mahdi Zununi Vahed, Sepideh Homaei Rad, Hamed Emdadi, Manijeh Akbarpour, Zahra Teshnehlab, Mohammad Pirmoradi, Saeed Alizadeh, Effat PLoS One Research Article OBJECTIVE: Thyroid Cancer (TC) is the most frequent endocrine malignancy neoplasm. It is the sixth cause of cancer in women worldwide. The treatment process could be expedited by identifying the controlling molecular mechanisms at the early and late stages, which can contribute to the acceleration of treatment schemes and the improvement of patient survival outcomes. In this work, we study the significant mRNAs through Machine Learning Algorithms in both the early and late stages of Papillary Thyroid Cancer (PTC). METHOD: During the course of our study, we investigated various methods and techniques to obtain suitable results. The sequence of procedures we followed included organizing data, using nested cross-validation, data cleaning, and normalization at the initial stage. Next, to apply feature selection, a t-test and binary Non-Dominated Sorting Genetic Algorithm II (NSGAII) were chosen to be employed. Later on, during the analysis stage, the discriminative power of the selected features was evaluated using machine learning and deep learning algorithms. Finally, we considered the selected features and utilized Association Rule Mining algorithm to identify the most important ones for improving the decoding of dominant molecular mechanisms in PTC through its early and late stages. RESULT: The SVM classifier was able to distinguish between early and late-stage categories with an accuracy of 83.5% and an AUC of 0.78 based on the identified mRNAs. The most significant genes associated with the early and late stages of PTC were identified as (e.g., ZNF518B, DTD2, CCAR1) and (e.g., lnc-DNAJB6-7:7, RP11-484D2.3, MSL3P1), respectively. CONCLUSION: Current study reveals a clear picture of the potential candidate genes that could play a major role not only in the early stage, but also throughout the late one. Hence, the findings could be of help to identify therapeutic targets for more effective PTC drug developments. Public Library of Science 2023-11-02 /pmc/articles/PMC10621943/ /pubmed/37917782 http://dx.doi.org/10.1371/journal.pone.0293335 Text en © 2023 Hosseiniyan Khatibi et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Hosseiniyan Khatibi, Seyed Mahdi
Zununi Vahed, Sepideh
Homaei Rad, Hamed
Emdadi, Manijeh
Akbarpour, Zahra
Teshnehlab, Mohammad
Pirmoradi, Saeed
Alizadeh, Effat
Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm
title Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm
title_full Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm
title_fullStr Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm
title_full_unstemmed Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm
title_short Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm
title_sort uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621943/
https://www.ncbi.nlm.nih.gov/pubmed/37917782
http://dx.doi.org/10.1371/journal.pone.0293335
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