@inproceedings{f5e9bfdfbd964dc0a2ef17370ff57f91,
title = "Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer",
abstract = "MicroRNAs (miRNAs) have significant biological roles at the molecular level by regulating genes post-transcriptionally. To understand the functional effects of miRNAs in different biological contexts, it is essential to elucidate miRNA-mRNA regulatory modules (MRMs). The computational complexity for inferencing MRMs is very high due to the many-to-many relationships between miRNAs and mRNAs and inferencing MRMs is still a challenging unresolved problem. In this paper, we propose a novel iterative segmented least square method for functional MRM discovery. Our method operates in two steps: 1) grouping and ordering the miRNAs and mRNAs to build per-sample matrices representing miRNA-mRNA regulations, and 2) determining maximum sized modules from structured miRNA-mRNA matrices. In experiments with human breast cancer data sets from TCGA, we show that our method outperforms existing methods in terms of both GO similarity and cluster evaluation. In addition, we show that modules determined by our method can be used for breast cancer survival prediction and subtype classification.",
keywords = "MicroRNA, Optimization, Regulatory network inference",
author = "Sungmin Rhee and Sangsoo Lim and Sun Kim",
note = "Publisher Copyright: {\textcopyright} 2016 IEEE.; 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 ; Conference date: 15-12-2016 Through 18-12-2016",
year = "2017",
month = jan,
day = "17",
doi = "10.1109/BIBM.2016.7822618",
language = "English",
series = "Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "767--770",
editor = "Kevin Burrage and Qian Zhu and Yunlong Liu and Tianhai Tian and Yadong Wang and Hu, {Xiaohua Tony} and Qinghua Jiang and Jiangning Song and Shinichi Morishita and Kevin Burrage and Guohua Wang",
booktitle = "Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016",
address = "United States",
}
