COMUNET: a tool to explore and visualize intercellular communication

Intercellular communication plays an essential role in multicellular organisms and several algorithms to analyse it from single-cell transcriptional data have been recently published, but the results are often hard to visualize and interpret. We developed COMUNET (Cell cOMmunication exploration with MUltiplex NETworks), a tool that streamlines the interpretation of the results from cell-cell communication analyses. COMUNET uses multiplex networks to represent and cluster all potential communication pathways between cell types. The algorithm also enables the search for specific patterns of communication and can perform comparative analysis between two biological conditions. To exemplify its use, here we apply COMUNET to investigate cell communication patterns in single-cell transcriptomic datasets from mouse embryos and from an acute myeloid leukemia patient at diagnosis and after treatment. Our algorithm is available on GitHub, along with all the code to perform the analysis reported.

• Publication year

  2019

• Venue

  bioRxiv

• Publication date

  2019-12-05

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btaa482PMID 32399572PMCID 7520036
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• talklr uncovers ligand-receptor mediated intercellular crosstalk

  2020cited by this paper
• Single-cell analysis targeting the proteome

  2020cited by this paper
• CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

  2020cited by this paper
• A map of tumor–host interactions in glioma at single-cell resolution

  2020cited by this paper
• Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.

  2019cited by this paper
• Arrayed molecular barcoding identifies TNFSF13 as a positive regulator of acute myeloid leukemia-initiating cells

  2019cited by this paper
• The emergent landscape of the mouse gut endoderm at single-cell resolution

  2019cited by this paper
• A MAP of tumor-host interactions in glioma at single cell resolution

  2019cited by this paper
• Systematic Identification of Cell-Cell Communication Networks in the Developing Brain

  2019cited by this paper
• Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche

  2019cited by this paper
• CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes

  2019cited by this paper
• Chemokines and Chemokine Receptors: New Targets for Cancer Immunotherapy

  2019cited by this paper
• Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming.

  2019cited by this paper
• Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting.

  2018cited by this paper
• The Head's Tale: Anterior-Posterior Axis Formation in the Mouse Embryo.

  2018cited by this paper
• Mapping the physical network of cellular interactions

  2018cited by this paper
• Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart.

  2018cited by this paper
• Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

  2018cited by this paper
• UMAP: Uniform Manifold Approximation and Projection

  2018cited by this paper
• Single-cell reconstruction of the early maternal–fetal interface in humans

  2018cited by this paper
• Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

  2018cited by this paper
• Acute Myeloid Leukemia and the Bone Marrow Niche—Take a Closer Look

  2018cited by this paper
• Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

  2017cited by this paper
• Complexity of bone marrow hematopoietic stem cell niche

  2017cited by this paper
• Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer.

  2017cited by this paper
• Social network architecture of human immune cells unveiled by quantitative proteomics

  2017cited by this paper
• Multilineage communication regulates human liver bud development from pluripotency

  2017cited by this paper
• Adipocyte Accumulation in the Bone Marrow during Obesity and Aging Impairs Stem Cell-Based Hematopoietic and Bone Regeneration

  2017cited by this paper
• Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung.

  2017cited by this paper
• Distinct bone marrow blood vessels differentially regulate hematopoiesis

  2016cited by this paper
• A Subset of Patients with Acute Myeloid Leukemia Has Leukemia Cells Characterized by Chemokine Responsiveness and Altered Expression of Transcriptional as well as Angiogenic Regulators

  2016cited by this paper
• Role of the tumor microenvironment in tumor progression and the clinical applications (Review).

  2016cited by this paper
• A draft network of ligand–receptor-mediated multicellular signalling in human

  2015cited by this paper
• Thymineless death in F10-treated AML cells occurs via lipid raft depletion and Fas/FasL co-localization in the plasma membrane with activation of the extrinsic apoptotic pathway.

  2015cited by this paper
• Hesperidin Inhibits Inflammatory Response Induced by Aeromonas hydrophila Infection and Alters CD4+/CD8+ T Cell Ratio

  2014cited by this paper
• The Inflammatory Chemokine CCL5 and Cancer Progression

  2014cited by this paper
• Megakaryocytes regulate hematopoietic stem cell quiescence via Cxcl4 secretion

  2013cited by this paper
• Keeping IGF-II under control: lessons from the IGF-II-IGF2R crystal structure.

  2009cited by this paper
• Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R

  2008cited by this paper
• Gene function in mouse embryogenesis: get set for gastrulation

  2007cited by this paper
• Parental imprinting of the mouse insulin-like growth factor II gene.

  1991cited by this paper
• THE DISTRIBUTION OF THE FLORA IN THE ALPINE ZONE.1

  1912cited by this paper

• Molecular basis for de novo thymus regeneration in a vertebrate, the axolotl.

  2025cites this paper
• Cell-cell communication inference and analysis: biological mechanisms, computational approaches, and future opportunities

  2025cites this paper
• Cell Type Based Cell-Cell Communication Inference via Multi-Scale Network Modeling

  2025cites this paper
• Differential cellular communication inference framework for large-scale single-cell RNA-sequencing data

  2025cites this paper
• Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions

  2025cites this paper
• New Insights and Implications of Cell–Cell Interactions in Developmental Biology

  2025cites this paper
• Charting spatial ligand-target activity using Renoir

  2024cites this paper
• An integrated approach identifies the molecular underpinnings of murine anterior visceral endoderm migration

  2024cites this paper
• The diversification of methods for studying cell–cell interactions and communication

  2024cites this paper
• CPPLS-MLP: a method for constructing cell–cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data

  2024cites this paper
• Community assesses differential cell communication using large multi-sample case-control scRNAseq datasets

  2024cites this paper
• MMCCI: multimodal integrative analysis of single-cell and spatial cell-type communications to uncover overarching and condition-specific ligand-receptor interaction pathways

  2024cites this paper
• exFINDER: identify external communication signals using single-cell transcriptomics data

  2023cites this paper
• exFINDER: identify external communication signals using single-cell transcriptomics data

  2023cites this paper
• Deep learning applications in single-cell genomics and transcriptomics data analysis.

  2023cites this paper
• ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods

  2023cites this paper
• scDiffCom: a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication

  2023cites this paper
• Sctensor detects many-to-many cell–cell interactions from single cell RNA-sequencing data

  2022cites this paper
• Cell-cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies

  2022cites this paper
• Trends & Opportunities in Visualization for Physiology: A Multiscale Overview

  2022cites this paper
• Dysregulated ligand–receptor interactions from single-cell transcriptomics

  2022cites this paper
• Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data

  2022cites this paper
• Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitors

  2021cites this paper
• The landscape of cell-cell communication through single-cell transcriptomics.

  2021cites this paper
• Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation.

  2021cites this paper
• The role of cell geometry and cell-cell communication in gradient sensing

  2021cites this paper
• Inferring and perturbing cell fate regulomes in human cerebral organoids

  2021cites this paper
• Characterisation of the transcriptional dynamics underpinning the function, fate, and migration of the mouse Anterior Visceral Endoderm

  2021influential citation