Identifying Essential Signature Genes and Expression Rules Associated With Distinctive Development Stages of Early Embryonic Cells

Lei Chen,Tao Zeng,Yu-Hang Zhang,Yu-Dong Cai,Xiaoyong Pan,Tao Huang

doi:10.1109/access.2019.2939556

Abstract

An embryo develops from a single-celled zygote, which produces a multi-cellular organism by mitosis. Due to the complication of processes and mechanisms, research on embryo cell clusters in different early embryo developmental stages with significant phenotypic differences is still lacking. In this work, we identified some gene characters and expression rules to classify these individual cells using several advanced computational methods. The single cell expression profiles of embryo cells were analyzed by the Monte Carlo feature selection (MCFS) method, resulting in a feature list. Then, the incremental feature selection (IFS) method, incorporating support vector machine (SVM), applied on such list to extract key gene characters. These gene characters include KHDC1, HMGN1, DCP, GDF9, RNF11, DNMT3L, and CDX1. Furthermore, a rule learning algorithm, Repeated Incremental Pruning to Produce Error Reduction (RIPPER), was applied to the informative features yielded by MCFS method, producing a group of classification rules. These rules can clearly uncover different expression patterns on cells in different stages. This study provided a group of effective gene signatures and rules for embryo cell subtyping and presented an applicable computational tool to further dig into the regulatory mechanisms of embryo development.

Highlights

An embryo develops from a zygote, which is produced by fertilization of female egg cell by the male sperm cell
To further select the discriminating features corresponding to different embryonic cell stages, we used incremental feature selection (IFS) with support vector machine (SVM) to classify the samples consisting of features from individually generated feature subsets based on the ranked feature list by Monte Carlo feature selection (MCFS)
As mentioned above, 3230 features have been screened to describe the optimal classifier for early embryo cells subtyping

Summary

Introduction

An embryo develops from a zygote, which is produced by fertilization of female egg cell by the male sperm cell. A multicellular organism was produced by mitosis, which is the early developmental period of a multi-cellular diploid eukaryotic organism. The development of zygote into an embryo goes through multiple stages, i.e., blastula, gastrula, and organogenesis. The associate editor coordinating the review of this manuscript and approving it for publication was Quan Zou. by a fluid-filled cavity, the blastocoel, which is surrounded by blastomeres. Blastula cells form two or three tissue layers by coordinated processes of cell division, invasion, and migration. Molecular and cellular interactions between germ layers prompt further differentiation of organ-specific cell types, based on the cells’ developmental potentials or competence to respond

Methods

Results

Conclusion