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All Journal EKSAKTA: Journal of Sciences and Data Analysis Media Statistika Jurnal Gaussian Jurnal Statistika Universitas Muhammadiyah Semarang TELKOMNIKA (Telecommunication Computing Electronics and Control) Bulletin of Electrical Engineering and Informatics Science and Technology Indonesia BAREKENG: Jurnal Ilmu Matematika dan Terapan JOURNAL OF APPLIED INFORMATICS AND COMPUTING Unisda Journal of Mathematics and Computer Science (UJMC) JTAM (Jurnal Teori dan Aplikasi Matematika) International Journal of Supply Chain Management Journal of Research Applications in Community Services Eduvest - Journal of Universal Studies Indonesian Journal of Mathematics and Applications Mathematical Journal of Modelling and Forecasting Indonesian Actuarial Journal
Adhitya Ronnie Effendie, Adhitya Ronnie
Departemen Matematika, FMIPA, Universitas Gadjah Mada
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Classification of Nicotine Treatment Response Based on Gene Expression Profiles Using Support Vector Machine and Gaussian Process Models Rahmadi Yotenka; Adhitya Ronnie Effendie; Gunardi Gunardi; Afiahayati Afiahayati; Aisha Ellany Midnova; Eugenia Rivanda Gita Flamboyan; Daninta Indiana Mahaputri; Leonardo Leonardo; Nayla Revania Dewayani; Muhammad Ahnaf Billie Chesta
Mathematical Journal of Modelling and Forecasting Vol. 4 No. 1 (2026): June 2026
Publisher : Universitas Negeri Padang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/mjmf.v4i1.50

Abstract

Nicotine is known to impair endothelial function and increase cardiovascular risk through transcriptional dysregulation. This study investigates the gene expression response of human induced pluripotent stem cell (iPSC)-derived endothelial cells to nicotine exposure using the RNA-seq dataset GSE274506. The analysis was conducted on 40 samples, consisting of 20 nicotine-treated and 20 untreated/control samples, using a 5-fold outer stratified cross-validation with 3-fold inner cross-validation for model tuning, reflecting the limited sample size relative to the high-dimensional gene expression feature space. Differential expression analysis identified 46 significant genes, comprising 28 upregulated and 18 downregulated, indicating perturbations in G protein-coupled receptor (GPCR) signaling, calcium homeostasis, and inflammatory processes. Functional enrichment analyses based on Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome consistently revealed dominant involvement of GPCR signaling, cyclic adenosine monophosphate (cAMP) signaling, calcium signaling, and transient receptor potential (TRP)-related pathways, suggesting a coordinated molecular response to nicotine-induced stress. To discriminate between nicotine-treated and control samples, Support Vector Machine (SVM) and Gaussian Process Classification (GPC) models were evaluated. The linear SVM achieved the best and most stable performance, with an accuracy of 0.875, an F1-score of 0.881, and a G-mean of 0.861, outperforming SVM with radial basis function kernels, single-kernel GPC variants, and a multiple kernel learning (MKL) GPC model. These findings indicate that the underlying transcriptomic structure of the data is predominantly linear, favoring linear kernel-based classifiers in high-dimensional gene expression analysis.
Co-Authors A'yun, Qonita Qurrota Abdul Talib Bon Abdurakhman Abdurakhman Abdurakhman Abdurakhman Afiahayati Afiahayati Aisha Ellany Midnova Anaviroh Anaviroh Danardono Danardono Dani, Andrea Tri Rian Daninta Indiana Mahaputri Dedi Rosadi Devni Prima Sari Eugenia Rivanda Gita Flamboyan Faihatuz Zuhairoh Fidia Deny Tisna Amijaya Gunardi Gunardi Hardina Sandariria Hartati indarsih, Indarsih Indradewa, Rhian Kariyam - Kariyam Kariyam Leonardo Leonardo Muhammad Ahnaf Billie Chesta Muhammad Iqbal Al-Banna Ismail Mulyadi, Taqriri Kamal Nayla Revania Dewayani Putra, Fachrian Bimantoro Rahmadi Yotenka Rohmatul Fajriyah Sandelvia, Krismona Saruan , Sandy Salomo Selvi Faristasari Sifriyani, Sifriyani Siswahyudianto Solikhatun, Solikhatun Sri Haryatmi Kartiko Sri Wahyuni Sukono Sukono Suryanto, Wiwit Susyanto, Nanang Syaripuddin Syaripuddin Uha Isnaini Wahyujati, Mohamad Fahruli Yotenka, Rahmadi Yuciana Wilandari Yuciana Wilandari Yulianti, Silvina Rosita Yulita, Tiara