Inference of genetic regulatory network for stem cell using single cells expression data

Jiangyong Wei, Xiaohua Hu, Xiufen Zou, Tianhai Tian

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

2 Citations (Scopus)

Abstract

Single cell experimental studies provide an unprecedented opportunity to examine the heterogeneity of molecular processes in different cells. However, the reconstruction of a sequence of changes in molecular processes and development of regulatory networks using single cell data are still challenging problems in bioinformatics and systems biology. In this work we propose an integrated framework to infer genetic regulatory networks using single cell experimental data. We first use the Wanderlust algorithm to construct the pseudo-trajectory of gene expression activities. Due to noise in the expression data, a Gauss process regression method is employed to produce a smoothly trajectory. Our integrated approach includes both a top-down approach (i.e. the GENIE3 algorithm) to infer the network structure and a bottom-up approach (i.e. differential equation model) to reverse-engineering the regulatory network. Using the gene network of hematopoietic development in the mouse embryo as the test problem, we developed a dynamic model for a network of nine genes. Our results suggest that the proposed integrated framework is an effective approach to reconstruct regulatory networks from single cell data.
Original languageEnglish
Title of host publicationProceedings 2016 IEEE International Conference on Bioinformatics and Biomedicine
EditorsTianhai Tian, Yadong Wang, Qinghua Jiang, Xiaohua Hu, Yunlong Liu, Shinichi Morishita, Kevin Burrage, Qian Zhu, Jiangning Song, Guohua Wang
Place of PublicationPiscataway NJ USA
PublisherIEEE, Institute of Electrical and Electronics Engineers
Pages217-222
Number of pages6
ISBN (Electronic)9781509016105
ISBN (Print)9781509016105
DOIs
Publication statusPublished - 2016
EventIEEE International Conference on Bioinformatics and Biomedicine 2016 - Kylin Villa Resort, Shenzhen, China
Duration: 15 Dec 201618 Dec 2016
Conference number: 8th
https://cci.drexel.edu/ieeebibm/bibm2016/

Conference

ConferenceIEEE International Conference on Bioinformatics and Biomedicine 2016
Abbreviated titleBIBM 2016
CountryChina
CityShenzhen
Period15/12/1618/12/16
Internet address

Keywords

  • gene regulatory network
  • single cell data
  • network inference
  • stem cell

Cite this

Wei, J., Hu, X., Zou, X., & Tian, T. (2016). Inference of genetic regulatory network for stem cell using single cells expression data. In T. Tian, Y. Wang, Q. Jiang, X. Hu, Y. Liu, S. Morishita, K. Burrage, Q. Zhu, J. Song, ... G. Wang (Eds.), Proceedings 2016 IEEE International Conference on Bioinformatics and Biomedicine (pp. 217-222). [7822521] Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/BIBM.2016.7822521