The intrinsic dimension of gene expression - Marta Biondo - Young Seminars SIFS скачать в хорошем качестве

The intrinsic dimension of gene expression - Marta Biondo - Young Seminars SIFS

The intrinsic dimension of gene expression during cell differentiation Marta Biondo, University of Catania and University of Palermo Abstract: The Waddington epigenetic landscape is a metaphor for the process of cell differentiation, depicting progenitor cells losing potency as they roll down a high-dimensional surface, eventually settling into terminally differentiated states. These cell states, or positions on the landscape, are basically defined by their gene expression profiles, which can be partially measured using single-cell RNA sequencing. However, the connection between this metaphor and large-scale transcriptomic data, including how to quantify the differentiation potential, remains open to question. In this talk, I will explore how statistical physics offers valuable analogies for interpreting such rugged landscapes. A key observable I will focus on is intrinsic dimensionality. High-dimensional data often concentrate on low-dimensional manifolds due to correlations, and I will demonstrate that the intrinsic dimensionality of gene expression datasets decreases during differentiation. This reduction reflects the narrowing of accessible expression space and serves as a robust, data-driven metric of cellular potency, independent of predefined marker genes. Through this approach, I aim to provide fresh insights into the geometry of the gene expression space during differentiation and its implications for developmental biology. Reference: https://doi.org/10.1101/2024.08.02.60... #YSSIFS