MyFX: A turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos

Ivan Montiel; Charlotte Konikoff; Bremen Braun; Mary Packard; Sian L. Gramates; Qian Sun; Jieping Ye; Sudhir Kumar

doi:10.1093/bioinformatics/btu007

MyFX: A turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos

Ivan Montiel, Charlotte Konikoff, Bremen Braun, Mary Packard, Sian L. Gramates, Qian Sun, Jieping Ye, Sudhir Kumar

Research output: Contribution to journal › Article › peer-review

Abstract

Summary: Spatial patterns of gene expression are of key importance in understanding developmental networks. Using in situ hybridization, many laboratories are generating images to describe these spatial patterns and to test biological hypotheses. To facilitate such analyses, we have developed biologist-centric software (myFX) that contains computational methods to automatically process and analyze images depicting embryonic gene expression in the fruit fly Drosophila melanogaster. It facilitates creating digital descriptions of spatial patterns in images and enables measurements of pattern similarity and visualization of expression across genes and developmental stages. myFX interacts directly with the online FlyExpress database, which allows users to search thousands of existing patterns to find co-expressed genes by image comparison.

Original language	English (US)
Pages (from-to)	1319-1321
Number of pages	3
Journal	Bioinformatics
Volume	30
Issue number	9
DOIs	https://doi.org/10.1093/bioinformatics/btu007
State	Published - May 1 2014

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btu007

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title = "MyFX: A turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos",

abstract = "Summary: Spatial patterns of gene expression are of key importance in understanding developmental networks. Using in situ hybridization, many laboratories are generating images to describe these spatial patterns and to test biological hypotheses. To facilitate such analyses, we have developed biologist-centric software (myFX) that contains computational methods to automatically process and analyze images depicting embryonic gene expression in the fruit fly Drosophila melanogaster. It facilitates creating digital descriptions of spatial patterns in images and enables measurements of pattern similarity and visualization of expression across genes and developmental stages. myFX interacts directly with the online FlyExpress database, which allows users to search thousands of existing patterns to find co-expressed genes by image comparison.",

author = "Ivan Montiel and Charlotte Konikoff and Bremen Braun and Mary Packard and Gramates, {Sian L.} and Qian Sun and Jieping Ye and Sudhir Kumar",

note = "Funding Information: Funding: US National Institutes of Health (HG002516-09 to S.K. and LM010730-03 to J.Y.). The source code of myFX is available upon request.",

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doi = "10.1093/bioinformatics/btu007",

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AU - Montiel, Ivan

AU - Konikoff, Charlotte

AU - Braun, Bremen

AU - Packard, Mary

AU - Gramates, Sian L.

AU - Sun, Qian

AU - Ye, Jieping

AU - Kumar, Sudhir

N1 - Funding Information: Funding: US National Institutes of Health (HG002516-09 to S.K. and LM010730-03 to J.Y.). The source code of myFX is available upon request.

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N2 - Summary: Spatial patterns of gene expression are of key importance in understanding developmental networks. Using in situ hybridization, many laboratories are generating images to describe these spatial patterns and to test biological hypotheses. To facilitate such analyses, we have developed biologist-centric software (myFX) that contains computational methods to automatically process and analyze images depicting embryonic gene expression in the fruit fly Drosophila melanogaster. It facilitates creating digital descriptions of spatial patterns in images and enables measurements of pattern similarity and visualization of expression across genes and developmental stages. myFX interacts directly with the online FlyExpress database, which allows users to search thousands of existing patterns to find co-expressed genes by image comparison.

AB - Summary: Spatial patterns of gene expression are of key importance in understanding developmental networks. Using in situ hybridization, many laboratories are generating images to describe these spatial patterns and to test biological hypotheses. To facilitate such analyses, we have developed biologist-centric software (myFX) that contains computational methods to automatically process and analyze images depicting embryonic gene expression in the fruit fly Drosophila melanogaster. It facilitates creating digital descriptions of spatial patterns in images and enables measurements of pattern similarity and visualization of expression across genes and developmental stages. myFX interacts directly with the online FlyExpress database, which allows users to search thousands of existing patterns to find co-expressed genes by image comparison.

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MyFX: A turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos

Abstract

ASJC Scopus subject areas

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