COMPARISON OF RNA-SEQUENCING AND RPPA DATA FOR CLASSIFICATION OF CANCER SUBTYPES

Year 2018, Volume: 20 Issue: 59, 606 - 621, 01.05.2018

Zerrin Işık

Abstract

Accurate identification of cancer subtypes of patients before their surgery will decrease diagnostic and treatment costs. The goal of this study is the identification of a limited number of biomarkers, which can predict subtypes of cancer patients who were diagnosed as lung or ovarian cancer, by using machine learning methods. For this purpose, a limited number of features were selected by using gene expression and protein level data, then supervised machine learning methods were trained with selected features, cancer subtype of a new patient was predicted by using these models. Support vector machines and random forest algorithms can classify cancer subtypes of new patients with the average accuracies of 87% - 95%. mRNA gene expression data provided the better classification results compared to the protein level data

Keywords

Cancer Classification, RNA-Sequencing

KANSER ALT-TÜRLERİNİN SINIFLANDIRILMASI İÇİN RNA-SEKANSLAMA VE RPPA VERİLERİNİN KARŞILAŞTIRILMASI

Abstract

Hastaların kanser alt-türlerini henüz ameliyat olmadan kesin doğrulukla tespit edilebilmek, tanı ve tedavi masraflarının azaltılmasını sağlayacaktır. Bu çalışmanın amacı, over ya da akciğer kanseri olduğu tespit edilen bir hastanın kanser alt-türünü tespit edebilecek belirli sayıdaki biyoişaretin makine öğrenmesi yöntemleriyle bulunmasıdır. Bu amaçla, mRNA gen ekspresyon ve protein seviyesi bilgileri kullanılarak kısıtlı sayıda öz-nitelik seçilmiş, bu öz-niteliklerle gözetimli makine öğrenmesi metotları eğitilmiş, bu modeller ile yeni gelen bir hastanın kanser alt-türü tahmin edilmiştir. Destek vektör makineleri ve rastgele orman algoritmaları, yeni kanser hastalarının kanser alt-türlerini ortalama %87 ile %95 arasında değişen doğruluk dereceleriyle sınıflandırabilmiştir. mRNA gen ekspresyon verisi protein seviyesi verisine göre, her iki kanser türünde de daha başarılı sınıflandırma sonuçları sağlamıştır

Keywords

Kanser Sınıflandırma, RNA-Sekanslama

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