Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks

Recent advances in single-cell RNA sequencing (scRNA-seq) have allowed researchers to explore transcriptional function at a cellular level. In this study, we present O_SCPLOWSCC_SCPLOWPPIN, a method for integrating single-cell RNA sequencing data with protein-protein interaction networks (PPINs) that detects active modules in cells of different transcriptional states. We achieve this by clustering RNA-sequencing data, identifying differentially expressed genes, constructing node-weighted PPINs, and finding the maximum-weight connected subgraphs with an exact Steiner-tree approach. As a case study, we investigate RNA-sequencing data from human liver spheroids but the techniques described here are applicable to other organisms and tissues. O_SCPLOWSCC_SCPLOWPPIN allows us to expand the output of differential expressed genes analysis with information from protein interactions. We find that different transcriptional states have different subnetworks of the PPIN significantly enriched which represent biological pathways. In these pathways, O_SCPLOWSCC_SCPLOWPPIN also identifies proteins that are not differentially expressed but have a crucial biological function (e.g., as receptors) and therefore reveals biology beyond a standard differentially expressed gene analysis.