期刊
IEEE ACCESS
卷 7, 期 -, 页码 128570-128578出版社
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
DOI: 10.1109/ACCESS.2019.2939556
关键词
Embryo development; single cell; expression pattern; rule; multi-class classification
资金
- Shanghai Municipal Science and Technology Major Project [2017SHZDZX01]
- National Key Research and Development Program of China [2018YFC0910403]
- National Natural Science Foundation of China [31701151]
- Natural Science Foundation of Shanghai [17ZR1412500]
- Shanghai Sailing Program [16YF1413800]
- Youth Innovation Promotion Association of Chinese Academy of Sciences (CAS) [2016245]
- Fund of the Key Laboratory of Stem Cell Biology of Chinese Academy of Sciences [201703]
- Science and Technology Commission of Shanghai Municipality (STCSM) [18dz2271000]
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.
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