PICASO: Profiling Integrative Communities of Aggregated Single-cell Omics data

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Various single-cell modalities covering transcriptomics, epigenetic and spatio-temporal changes in health and disease phenotypes are used in an exploratory way to understand biological systems at single-cell resolution. However, the vast amount of such single-cell data is not systematically linked to existing biomedical data. Networks have previously been used to represent harmonized biomedical data. Integrating various resources of biomedical data in networks has recently received increasing attention. These aggregated networks can provide additional insight into the biology of complex human diseases at cell-type level, however, lack inclusion of single cell expression data. Here, we present the PICASO framework, which incorporates single-cell gene expression data as an additional layer to represent associations between cell types, disease phenotypes, drugs and genes. The PICASO network includes several standardized biomedical databases such as STRING, Uniprot, GeneOntology, Reactome, OmniPath and OpenTargets. Using multiple cell type-specific instances of the framework, each annotated and scored with their respective expression data, comparisons between disease states can be made by computing respective sub-networks and comparing the expression scores between conditions. Ultimately, these group-specific networks will allow the identification of relevant genes, processes and potentially druggable targets, as well as the comparison of different measured groups and thus the identification of group-specific communities and interactions.

Authors 3

1. Markus Joppich

   Ludwig-Maximilians-Universität München

   Affiliation as printed

   Institute for Informatics, Ludwig-Maximilians-Universität München

   LMU Munich;

   LMU Munich

2. Rafael Kramann Aachen Department of Medicine 2 (Nephrology Clinical Immunology and Hypertension)

   RWTH Aachen University

   Affiliation as printed

   Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center

   Department of Medicine 2 (Nephrology, Rheumatology, Clinical Immunology and Hypertension), RWTH Aachen University, Medical Faculty

   RWTH Aachen University

3. Sikander Hayat corresponding Aachen Department of Medicine 2 (Nephrology Clinical Immunology and Hypertension)

   RWTH Aachen University

   Affiliation as printed

   Department of Medicine 2 (Nephrology, Rheumatology, Clinical Immunology and Hypertension), RWTH Aachen University, Medical Faculty

   RWTH Aachen University