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Image analysis and empirical modeling of gene and protein expression

Trisnadi, Nathanie and Altinok, Alphan and Stathopoulos, Angelike and Reeves, Gregory T. (2013) Image analysis and empirical modeling of gene and protein expression. Methods, 62 (1). pp. 68-78. ISSN 1046-2023. PMCID PMC3807737. doi:10.1016/j.ymeth.2012.09.016. https://resolver.caltech.edu/CaltechAUTHORS:20130919-123938211

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Abstract

Protein gradients and gene expression patterns are major determinants in the differentiation and fate map of the developing embryo. Here we discuss computational methods to quantitatively measure the positions of gene expression domains and the gradients of protein expression along the dorsal–ventral axis in the Drosophila embryo. Our methodology involves three layers of data. The first layer, or the primary data, consists of z-stack confocal images of embryos processed by in situ hybridization and/or antibody stainings. The secondary data are relationships between location, usually an x-axis coordinate, and fluorescent intensity of gene or protein detection. Tertiary data comprise the optimal parameters that arise from fits of the secondary data to empirical models. The tertiary data are useful to distill large datasets of imaged embryos down to a tractable number of conceptually useful parameters. This analysis allows us to detect subtle phenotypes and is adaptable to any set of genes or proteins with a canonical pattern. For example, we show how insights into the Dorsal transcription factor protein gradient and its target gene ventral-neuroblasts defective (vnd) were obtained using such quantitative approaches.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1016/j.ymeth.2012.09.016 DOIArticle
http://www.sciencedirect.com/science/article/pii/S1046202312002629PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807737/PubMed CentralArticle
ORCID:
AuthorORCID
Trisnadi, Nathanie0000-0003-0920-1282
Stathopoulos, Angelike0000-0001-6597-2036
Additional Information:© 2012 Elsevier Inc. Available online 24 October 2012. Communicated by David Arnosti. We are grateful to Marcos Nahmad for providing the embryo image used in Fig. 10.We also thank Francois Nedelec for the development of the tiffread2c to load lsm-based images into Matlab, and Peter Li for the LSM Filetoolbox to read metadata from lsm files into Matlab. This work was supported by a postdoctoral fellowship from the Jane Coffin Childs Memorial Fellowship for Medical Research to G.T.R.; by the Arnold and Mabel Beckman Foundation, the California Institute of Technology, and a gift from Peter Cross to A.A.; and by Grant R01 GM077668 from the NIGMS to A.S.
Funders:
Funding AgencyGrant Number
Jane Coffin Childs Memorial Fund for Medical ResearchUNSPECIFIED
Arnold and Mabel Beckman FoundationUNSPECIFIED
CaltechUNSPECIFIED
NIHR01 GM077668
Peter CrossUNSPECIFIED
Subject Keywords:Quantitative measurements; Gene expression; Protein gradient; Drosophila melanogaster; Dorsal-ventral patterning; Empirical modeling
Issue or Number:1
PubMed Central ID:PMC3807737
DOI:10.1016/j.ymeth.2012.09.016
Record Number:CaltechAUTHORS:20130919-123938211
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20130919-123938211
Official Citation:Nathanie Trisnadi, Alphan Altinok, Angelike Stathopoulos, Gregory T. Reeves, Image analysis and empirical modeling of gene and protein expression, Methods, Volume 62, Issue 1, 15 July 2013, Pages 68-78, ISSN 1046-2023, http://dx.doi.org/10.1016/j.ymeth.2012.09.016. (http://www.sciencedirect.com/science/article/pii/S1046202312002629)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:41416
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:19 Sep 2013 19:48
Last Modified:10 Nov 2021 04:29

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