Geometry of the Gene Expression Space of Individual Cells

• DOI: 10.1371/journal.pcbi.1004224
• Publication Date: 2015-07-10T18:37:34Z
• Authors: Yael Korem; Pablo Szekely; Yuval Hart; Hila Sheftel; Jean Hausser; Avi Mayo; Michael E. Rothen...; Tomer Kalisky; Uri Alon
• Keywords: Tetrahedron; Polyhedron

There is a revolution in the ability to analyze gene expression of single cells tissue. To understand this data we must comprehend how are distributed high-dimensional space. One open question whether cell types form discrete clusters or forms continuum states. If such exists, what its geometry? Recent theory on evolutionary trade-offs suggests that need perform multiple tasks arranged polygon polyhedron (line, triangle, tetrahedron and so on, generally called polytopes) space, whose vertices profiles optimal for each task. Here, single-cell from human mouse tissues profiled using variety technologies. We fit shapes with different numbers vertices, compute their statistical significance, infer tasks. find cases which fill out states within polyhedron. This occurs intestinal progenitor cells, The four enriched genes specific task related stemness early differentiation. A polyhedral also found spleen dendritic known immune tasks: correspond key maturation, pathogen sensing communication lymphocytes. mixture continuum-like distributions other types, including bone marrow differentiated crypt cells. approach can be used geometry biological wide range datasets. present results suggest concept type may expanded. In addition discreet gene-expression new possibility: polyhedron, represent specialists at