Friday, 13 October 2017 10:45

KU LEUVEN: Cell type identification with SCENIC Featured

A team from the Lab of Computational Biology (LCB) at Katholieke Universiteit Leuven, Belgium, led by Computational biologist Prof. Stein Aerts has developed a computer program called SCENIC that is able to identify different cell types based on their gene expression patterns, quickly and accurately.

The program allows a better understanding of how the fate of the cell types is regulated, and for the identification of master regulators, which could also be potential drug targets.

SCENIC is a workflow in R to infer gene regulatory networks and identify cell states from single-cell RNA-seq data. It allow them to systematically study the biological changes associated with different diseases, to understand where disease-associated genes are active in human´s bodies, analyse the molecular mechanisms that govern the production and activity of different cell types, and sort out how different cell types combine and work together to form tissues.

The team has already applied the method to brain tissue of mice and humans. They also used it to analyse and compare cancer cells from brain and skin tumours, which led to the identification of new cell types related to metastasis.

The method could help develop the Human Cell Atlas, a global effort aimed at mapping all different cell types and states in the human body.

Original publication:
Aibar S, Bravo Gonzalez-Blas C, Moerman T, Wouters J, Huynh-Thu VA, Imrichova H, Kalender Atak Z, Hulselmans G, Dewaele M, Rambow F, Geurts P, Aerts J, Marine C, van den Oord J, Aerts S. (2017): SCENIC: Single-cell regulatory network inference and clustering. Nature Methods. 2017 Oct 9; Epub ahead of print. doi: 10.1038/nmeth.4463

Source and more information:
https://sciencebusiness.net/network-news/computer-programme-detects-differences-between-human-cells
https://gbiomed.kuleuven.be/english/research/50000622/lcb/tools/scenic