Apr 2, 2020

Comparative single-cell trajectory network enrichment identifies pseudo-temporal systems biology patterns in hematopoiesis and CD8 T-cell development

BioRxiv : the Preprint Server for Biology
Alexander G. B. GroenningJ. Baumbach

Abstract

Single cell transcriptomics (scRNA-seq) technologies allow for investigating cellular processes on an unprecedented resolution. While software packages for scRNA-seq raw data analysis exist, no method for the extraction of systems biology signatures that drive different pseudo-time trajectories exists. Hence, pseudo-temporal molecular sub-network expression profiles remain undetermined, thus, hampering our understanding of the molecular control of cellular development on a single cell resolution. We have developed Scellnetor, the first network-constraint time-series clustering algorithm implemented as interactive webtool to identify modules of genes connected in a molecular interaction network that show differentiating temporal expression patterns. Scellnetor allows selecting two differentiation courses or two developmental trajectories for comparison on a systems biology level. Scellnetor identifies mechanisms driving hematopoiesis in mouse and mechanistically interpretable subnetworks driving dysfunctional CD8 T-cell development in chronic infections. Scellnetor is the first method to allow for single cell trajectory network enrichment for systems level hypotheses generation, thus lifting scRNA-seq data analysis to a systems ...Continue Reading

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Mentioned in this Paper

Metabolic Process, Cellular
Enzymes, antithrombotic
Regulation of Biological Process
Amino Acids, I.V. solution additive
Transcription, Genetic
Enzymes for Treatment of Wounds and Ulcers
Analysis
Genetic Translation Process
Enzymes, hematological
Enzymology

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