# Variations in the Intragene Methylation Profiles Hallmark Induced Pluripotency

## TL;DR

This paper shows how methylation patterns can be used to distinguish between embryonic and induced pluripotent stem cells with high accuracy using machine learning.

## Contribution

A novel feature selection method based on classifier accuracy is proposed, achieving over 95% classification accuracy.

## Key findings

- Intragene methylation measures can differentiate embryonic and induced pluripotent stem cells with over 95% accuracy.
- Selected features are enriched with genes related to stemness and cancer discrimination.
- The method can be applied broadly to classify cells based on methylation profiles.

## Abstract

We demonstrate the potential of differentiating embryonic and induced pluripotent stem cells by the regularized linear and decision tree machine learning classification algorithms, based on a number of intragene methylation measures. The resulting average accuracy of classification has been proven to be above 95%, which overcomes the earlier achievements. We propose a constructive and transparent method of feature selection based on classifier accuracy. Enrichment analysis reveals statistically meaningful presence of stemness group and cancer discriminating genes among the selected best classifying features. These findings stimulate the further research on the functional consequences of these differences in methylation patterns. The presented approach can be broadly used to discriminate the cells of different phenotype or in different state by their methylation profiles, identify groups of genes constituting multifeature classifiers, and assess enrichment of these groups by the sets of genes with a functionality of interest.