From spatial-data to 3D models of the developing human brain.
Visualisation and interpretation of gene expression data have been crucial to advances in our understanding of mechanisms underlying early brain development. As most developmental processes involve complex changes in size, shape and structure, spatial-data can most readily provide information at multiple levels (cell type, cell location in relation to tissue organisation or body axes, etc.), that can be related to these complex changes. Although three-dimensional (3D) spatial-data are ideal, the restricted availability of suitable tissues makes it difficult to generate these for genes expressed at early human fetal stages. Mapping gene expression data to representative 3D models facilitates combinatorial analysis of multiple expression patterns but does not overcome the problems of sparsely sampled data in time and space. Here we describe software that allows 3D domains to be reconstructed by interpolating between sparse 2D gene expression patterns that have been mapped to 3D representative models of corresponding human developmental stages. A set of procedures are proposed to infer expression domains in these gaps. The procedures, which are connected in a serial way, include components clustering, components tracking, shape matching and points interpolation. Each procedure consists of a graphical user interface and a set of algorithms. Results on exemplar gene data are provided.
Institute of Human Genetics, Newcastle University, UK. xunxian.wang@ncl.ac.uk
Xunxian
X
Wang
Susan
S
Lindsay
Richard
R
Baldock
D001921:Brain / Q000378:metabolism*; D001931:Brain Mapping / Q000379:methods; D016000:Cluster Analysis; D019295:Computational Biology; D003196:Computer Graphics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D007090:Image Interpretation, Computer-Assisted; D021621:Imaging, Three-Dimensional; D017403:In Situ Hybridization; D012984:Software; D013997:Time Factors; D014584:User-Computer Interface