Inference of Gene Co-expression Networks from Single-Cell RNA-Sequencing Data

  • Alicia T. LamereEmail author
  • Jun Li
Part of the Methods in Molecular Biology book series (MIMB, volume 1935)


Single-cell RNA-Sequencing is a pioneering extension of bulk-based RNA-Sequencing technology. The “guilt-by-association” heuristic has led to the use of gene co-expression networks to identify genes that are believed to be associated with a common cellular function. Many methods that were developed for bulk-based RNA-Sequencing data can continue to be applied to single-cell data, and several of the most widely used methods are explored. Several methods for leveraging the novel time information contained in single-cell data when constructing gene co-expression networks, which allows for the incorporation of directed associations, are also discussed.

Key words

Gene co-expression network Gene regulatory network Single-cell RNA-Seq Correlation coefficient Count data Directed network Pseudotime 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Mathematics DepartmentBryant UniversitySmithfieldUSA
  2. 2.Applied and Computational Mathematics and Statistics DepartmentUniversity of Notre DameNotre DameUSA

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