SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data.

Change log
Woodhouse, Steven 
Piterman, Nir 
Wintersteiger, Christoph M  ORCID logo
Gottgens, Berthold 
Fisher, Jasmin 

Background Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and disease processes. New ambitious efforts like the Human Cell Atlas will soon lead to an explosion of data with potential for uncovering and understanding the regulatory networks which underlie the behaviour of all human cells. In order to take advantage of this data, however, there is a need for general-purpose, user-friendly and efficient computational tools that can be readily used by biologists who do not have specialist computer science knowledge. Results The Single Cell Network Synthesis toolkit (SCNS) is a general-purpose computational tool for the reconstruction and analysis of executable models from single-cell gene expression data. Through a graphical user interface, SCNS takes single-cell qPCR or RNA-sequencing data taken across a time course, and searches for logical rules that drive transitions from early cell states towards late cell states. Because the resulting reconstructed models are executable, they can be used to make predictions about the effect of specific gene perturbations on the generation of specific lineages. Conclusions SCNS should be of broad interest to the growing number of researchers working in single-cell genomics and will help further facilitate the generation of valuable mechanistic insights into developmental, homeostatic and disease processes.

Genomics, Algorithms, Computer Graphics, User-Computer Interface, Gene Regulatory Networks, Single-Cell Analysis
Journal Title
BMC systems biology
Conference Name
Journal ISSN
Volume Title
BioMed Central
MRC (MC_PC_12009)
Research in the Gottgens lab is supported by infrastructure support funding from the Wellcome Trust to the Wellcome Trust and MRC Cambridge Stem Cell Institute. Steven Woodhouse is a postdoctoral researcher supported by Microsoft Research