Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings

Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings

Mahfouz, A.M.E.T.A.
Van de Giessen, M.
Van der Maaten, L.J.P.
Huisman, S.M.H.
Reinders, M.J.T.
Hawrylycz, M.J.
Lelieveldt, B.P.F.

Electrical Engineering, Mathematics and Computer Science

Intelligent Systems

2014-10-16

The Allen Brain Atlases enable the study of spatially resolved, genome-wide gene expression patterns across the mammalian brain. Several explorative studies have applied linear dimensionality reduction methods such as Principal Component Analysis (PCA) and classical Multi-Dimensional Scaling (cMDS) to gain insight into the spatial organization of these expression patterns. In this paper, we describe a non-linear embedding technique called Barnes-Hut Stochastic Neighbor Embedding (BH-SNE) that emphasizes the local similarity structure of high-dimensional data points. By applying BH-SNE to the gene expression data from the Allen Brain Atlases, we demonstrate the consistency of the 2D, non-linear embedding of the sagittal and coronal mouse brain atlases, and across 6 human brains. In addition, we quantitatively show that BH-SNE maps are superior in their separation of neuroanatomical regions in comparison to PCA and cMDS. Finally, we assess the effect of higher-order principal components on the global structure of the BH-SNE similarity maps. Based on our observations, we conclude that BH-SNE maps with or without prior dimensionality reduction (based on PCA) provide comprehensive and intuitive insights in both the local and global spatial transcriptome structure of the human and mouse Allen Brain Atlases.

Allen Brain Atlas
spatial-mapped gene expression
brain transcriptome structure
dimensionality reduction
Stochastic Neighbor Embedding

http://resolver.tudelft.nl/uuid:e8921b7d-f463-4f7a-a729-50f7a622834a

https://doi.org/10.1016/j.ymeth.2014.10.004

Elsevier

1046-2023

Methods, 73, 2015

Institutional Repository

journal article

(c) 2014 The Authors
This is an open access article under the CC BY-NC-ND license