A methodology to infer gene networks from spatial patterns of expression - an application to fluorescence in situ hybridization images

Author(s)

Campiteli, Monica Guimaraes ^[1] ; Comin, Cesar Henrique ^[1] ; Costa, Luciano da Fontoura ^[1] ; Babu, M. Madan ^[2] ; Cesar, Jr., Roberto Marcondes ^[3]

Affiliation

^[1] Univ Sao Paulo, Inst Fis Sao Carlos, Sao Carlos, SP - Brazil

^[2] MRC, Mol Biol Lab, Cambridge CB2 0QH - England

^[3] Univ Sao Paulo, Inst Matemat & Estat, Sao Paulo - Brazil

• Document type: Journal article
• Source: MOLECULAR BIOSYSTEMS; v. 9, n. 7, p. 1926-1930, 2013.
• Web of Science Citations: 0

Abstract

The proper functional development of a multicellular organism depends on an intricate network of interacting genes that are expressed in accurate temporal and spatial patterns across different tissues. Complex inhibitory and excitatory interactions among genes control the territorial differences that explain specialized cell fates, embryo polarization and tissues architecture in metazoans. Given the nature of the regulatory gene networks, similarity of expression patterns can identify genes with similar roles. The inference and analysis of the gene interaction networks through complex network tools can reveal important aspects of the biological system modeled. Here we suggest an image analysis pipeline to quantify co-localization patterns in in situ hybridization images of Drosophila embryos and, based on these patterns, infer gene networks. We analyze the spatial dispersion of the gene expression and show the gene interaction networks for different developmental stages. Our results suggest that the inference of developmental networks based on spatial expression data is biologically relevant and represents a potential tool for the understanding of animal development. (AU)

• FAPESP's process: 11/22639-8 - Unveiling the relationship between structure and dynamics on modular networks
• Grantee: Cesar Henrique Comin
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 05/00587-5 - Mesh (graph) modeling and techniques of pattern recognition: structure, dynamics and applications
• Grantee: Roberto Marcondes Cesar Junior
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 99/12765-2 - Development and assessment of novel and accurate methods in shape analysis and computer vision
• Grantee: Luciano da Fontoura Costa
• Support Opportunities: Research Projects - Thematic Grants