scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data

Jakobsson, Jon E. T.Uppsala universitet,Lagerström: Sensoriska kretsar (författare)

scConnect : a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data

MotivationCell to cell communication is critical for all multicellular organisms, and single-cell sequencing facilitates the construction of full connectivity graphs between cell types in tissues. Such complex data structures demand novel analysis methods and tools for exploratory analysis.ResultsWe propose a method to predict the putative ligand–receptor interactions between cell types from single-cell RNA-sequencing data. This is achieved by inferring and incorporating interactions in a multi-directional graph, thereby enabling contextual exploratory analysis. We demonstrate that our approach can detect common and specific interactions between cell types in mouse brain and human tumors, and that these interactions fit with expected outcomes. These interactions also include predictions made with molecular ligands integrating information from several types of genes necessary for ligand production and transport. Our implementation is general and can be appended to any transcriptome analysis pipeline to provide unbiased hypothesis generation regarding ligand to receptor interactions between cell populations or for network analysis in silico.Availability and implementationscConnect is open source and available as a Python package at https://github.com/JonETJakobsson/scConnect. scConnect is directly compatible with Scanpy scRNA-sequencing pipelines.

MEDICIN OCH HÄLSOVETENSKAP Medicinska och farmaceutiska grundvetenskaper Neurovetenskaper hsv//swe
MEDICAL AND HEALTH SCIENCES Basic Medicine Neurosciences hsv//eng
Computational Mathematics
Computational Theory and Mathematics
Computer Science Applications
Molecular Biology
Biochemistry
Statistics and Probability
Bioinformatik
Bioinformatics

Spjuth, Ola,Professor,1977-Uppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)olspj499 (författare)
Lagerström, Malin C.Uppsala universitet,Lagerström: Sensoriska kretsar(Swepub:uu)malag504 (författare)
Uppsala universitetLagerström: Sensoriska kretsar (creator_code:org_t)

Ingår i:Bioinformatics: Oxford University Press37:20, s. 3501-35081367-48031367-48111460-2059

Av författaren/redakt...: Jakobsson, Jon E ...; Spjuth, Ola, Pro ...; Lagerström, Mali ...

Om ämnet

MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Medicinska och f ...; och Neurovetenskaper

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