Name
Title | ||
|---|---|---|
Analysis of temporal-spatial co-variation within gene expression microarray data in an organogenesis model |
Abstract | ||
|---|---|---|
The gene networks underlying closure of the optic fissure during vertebrate eye development are poorly understood. We used a novel clustering method based on Laplacian Eigenmaps, a nonlinear dimension reduction method, to analyze microarray data from laser capture microdissected (LCM) cells at the site and developmental stages (days 10.5 to 12.5) of optic fissure closure. Our new method provided greater biological specificity than classical clustering algorithms in terms of identifying more biological processes and functions related to eye development as defined by Gene Ontology at lower false discovery rates. This new methodology builds on the advantages of LCM to isolate pure phenotypic populations within complex tissues and allows improved ability to identify critical gene products expressed at lower copy number. The combination of LCM of embryonic organs, gene expression microarrays, and extracting spatial and temporal co-variations appear to be a powerful approach to understanding the gene regulatory networks that specify mammalian organogenesis. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1007/978-3-642-13078-6_6 | ISBRA |
Keywords | Field | DocType |
biological process,greater biological specificity,gene expression microarrays,gene expression microarray data,eye development,organogenesis model,gene regulatory network,classical clustering algorithm,critical gene product,new method,gene network,nonlinear dimension reduction method,temporal-spatial co-variation,laser capture microdissection,microarray data,gene expression,false discovery rate,dimension reduction,copy number | Gene,Eye development,Microarray,Biology,Microarray analysis techniques,Bioinformatics,Gene regulatory network,Cluster analysis,Biological specificity,DNA microarray | Conference |
Volume | ISSN | ISBN |
6053 | 0302-9743 | 3-642-13077-1 |
Citations | PageRank | References |
3 | 0.45 | 4 |
Authors | ||
7 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Martin Ehler | 1 | 89 | 14.41 |
| Vinodh N. Rajapakse | 2 | 21 | 2.47 |
| Barry R Zeeberg | 3 | 17 | 2.35 |
| Brian Brooks | 4 | 3 | 0.79 |
| Jacob D. Brown | 5 | 14 | 0.89 |
| Wojciech Czaja | 6 | 29 | 6.05 |
| Robert F. Bonner | 7 | 20 | 2.42 |