Can I read Sepal : Identifying Transcript Profiles with Spatial Patterns by Diffusion-based Modeling on EtoBox?

Sepal : Identifying Transcript Profiles with Spatial Patterns by Diffusion-based Modeling by Alma Andersson; Joakim Lundeberg is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Sepal : Identifying Transcript Profiles with Spatial Patterns by Diffusion-based Modeling about?

## Abstract ## Motivation Collection of spatial signals in large numbers has become a routine task in multiple omics-fields, but parsing of these rich datasets still pose certain challenges. In whole or near-full transcriptome spatial techniques, spurious expression profiles are intermixed with those exhibiting an organized structure. To distinguish profiles with spatial patterns from the background noise, a metric that enables quantification of spatial structure is desirable. Current methods designed for similar purposes tend to be built around a framework of statistical hypothesis testing, hence we were compelled to explore a fundamentally different strategy. ## Results We propose an unexplored approach to analyze spatial transcriptomics data, simulating diffusion of individual transcripts to extract genes with spatial patterns. The method performed as expected when presented with synthetic data. When applied to real data, it identified genes with distinct spatial profiles, involved in key biological processes or characteristic for certain cell types. Compared to existing methods, ours seemed to be less informed by the genes’ expression levels and showed better time performance w

Who reads Sepal : Identifying Transcript Profiles with Spatial Patterns by Diffusion-based Modeling?

Author

Alma Andersson; Joakim Lundeberg

Publisher

Oxford University Press (OUP)

Published

2021

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)