School of Computer Science, Carnegie Mellon Unversity, Pittsburgh, PA, USA.
Bioinformatics. 2010 Jun 15;26(12):i47-56. doi: 10.1093/bioinformatics/btq172.
Microarray profiling of mRNA abundance is often ill suited for temporal-spatial analysis of gene expressions in multicellular organisms such as Drosophila. Recent progress in image-based genome-scale profiling of whole-body mRNA patterns via in situ hybridization (ISH) calls for development of accurate and automatic image analysis systems to facilitate efficient mining of complex temporal-spatial mRNA patterns, which will be essential for functional genomics and network inference in higher organisms.
We present SPEX(2), an automatic system for embryonic ISH image processing, which can extract, transform, compare, classify and cluster spatial gene expression patterns in Drosophila embryos. Our pipeline for gene expression pattern extraction outputs the precise spatial locations and strengths of the gene expression. We performed experiments on the largest publicly available collection of Drosophila ISH images, and show that our method achieves excellent performance in automatic image annotation, and also finds clusters that are significantly enriched, both for gene ontology functional annotations, and for annotation terms from a controlled vocabulary used by human curators to describe these images.
Software will be available at http://www.sailing.cs.cmu.edu/.
Supplementary data are available at Bioinformatics online.
微阵列分析 mRNA 丰度通常不适合对多细胞生物（如果蝇）的基因表达进行时空分析。通过原位杂交 (ISH) 进行基于图像的全基因组 mRNA 模式分析的最新进展呼吁开发准确和自动的图像分析系统，以方便有效地挖掘复杂的时空 mRNA 模式，这对于高等生物的功能基因组学和网络推断至关重要。
我们提出了 SPEX(2)，这是一个用于胚胎 ISH 图像处理的自动系统，它可以提取、转换、比较、分类和聚类果蝇胚胎中的空间基因表达模式。我们的基因表达模式提取管道输出基因表达的精确空间位置和强度。我们在最大的公开果蝇 ISH 图像集合上进行了实验，结果表明我们的方法在自动图像注释方面表现出色，并且还发现了显著富集的聚类，无论是针对基因本体功能注释，还是针对用于描述这些图像的受控词汇表中的注释术语。
软件将可在 http://www.sailing.cs.cmu.edu/ 获得。
补充数据可在生物信息学在线获得。
