Determination of cell pluripotency by integrating protein-protein interaction networks and sc-RNAseq data

SENRA, DANIELA; GUISONI, NARA; DIAMBRA, LUIS

Simposio; Human Cell Atlas LATAM 2022 Symposium; 2022

Human Cell Atlas

https://www.youtube.com/watch?v=SC7Ww_gNf2o&list=PLkef4SGmngdZ8eqXrvnN_LA5WBKMTsgMDESTE CONGRESO FUE VIRTUAL Y LA PRESENTACION ORAL ESTA EN EL LINK ARRIBA, QUE NO PUEDO ADJUNTAR COMO ARCHIVO. SIGUE ABAJO EL ABSTRACTTrajectory inference is a common application of scRNA-seq data. However, it is often necessary to previously determine the origin of the trajectories, the stem or progenitor cells. In this work, we propose a computational tool to quantify pluripotency from single cell transcriptomics data. This approach uses the protein-protein interaction (PPI) network associated with the differentiation process as a scaffold and the gene expression matrix to calculate a score that we call differentiation activity. This score reflects how active the differentiation network is in each cell. We benchmark the performance of our algorithm with two previously published tools, LandSCENT (Chen et al., 2019) and CytoTRACE (Gulati et al., 2020), for four healthy human data sets: breast, colon, hematopoietic and lung. We show that our algorithm is more efficient than LandSCENT and requires less RAM memory than the other programs. We also illustrate a complete workflow from the count matrix to trajectory inference using the breast data set.