Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone

Kumar, Sudhir; Boccia, Kelly; McCutchan, Michael; Ye, Jieping

doi:10.1093/bioinformatics/bts518

Cited by 10 publications

(4 citation statements)

References 7 publications

(9 reference statements)

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“…In addition to categorizing embryo images into finer sub-stages, our stage score can help to sort all embryo images based on their estimated developmental time (refer to Supplementary Materials for more results on embryo sorting). This will add great functionalities to our current FlyExpress database, and a preliminary version is already included in our iPhone app ( Kumar et al , 2012 ).…”

Section: Resultsmentioning

confidence: 99%

Automated annotation of developmental stages ofDrosophilaembryos in images containing spatial patterns of expression

Yuan

Cheng

et al. 2013

Bioinformatics

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Motivation: Drosophila melanogaster is a major model organism for investigating the function and interconnection of animal genes in the earliest stages of embryogenesis. Today, images capturing Drosophila gene expression patterns are being produced at a higher throughput than ever before. The analysis of spatial patterns of gene expression is most biologically meaningful when images from a similar time point during development are compared. Thus, the critical first step is to determine the developmental stage of an embryo. This information is also needed to observe and analyze expression changes over developmental time. Currently, developmental stages (time) of embryos in images capturing spatial expression pattern are annotated manually, which is time- and labor-intensive. Embryos are often designated into stage ranges, making the information on developmental time course. This makes downstream analyses inefficient and biological interpretations of similarities and differences in spatial expression patterns challenging, particularly when using automated tools for analyzing expression patterns of large number of images.Results: Here, we present a new computational approach to annotate developmental stage for Drosophila embryos in the gene expression images. In an analysis of 3724 images, the new approach shows high accuracy in predicting the developmental stage correctly (79%). In addition, it provides a stage score that enables one to more finely annotate each embryo so that they are divided into early and late periods of development within standard stage demarcations. Stage scores for all images containing expression patterns of the same gene enable a direct way to view expression changes over developmental time for any gene. We show that the genomewide-expression-maps generated using images from embryos in refined stages illuminate global gene activities and changes much better, and more refined stage annotations improve our ability to better interpret results when expression pattern matches are discovered between genes.Availability and implementation: The software package is available for download at: http://www.public.asu.edu/∼jye02/Software/Fly-Project/.Contact: jieping.ye@asu.eduSupplementary information: Supplementary data are available at Bioinformatics online.

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Section: Resultsmentioning

confidence: 99%

Automated annotation of developmental stages ofDrosophilaembryos in images containing spatial patterns of expression

Yuan

Cheng

et al. 2013

Bioinformatics

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“…One is Fly-FISH (http://fly-fish.ccbr.utoronto.ca/), a database documents the expression and localization patterns of Drosophila mRNAs at the cellular and subcellular level during early embryogenesis and third instar larval tissues ( Figures 2G-M) (23,24). The other is FlyExpress (http://www.flyexpress.net/), a freely approachable online knowledgebase offering users an occasion to investigate and analyze expression patterns of developmental genes in Drosophila embryogenesis (Figures 2A-F) (25)(26)(27). According to the FLY-FISH or FlyExpress databases, there are 15 LIM genes expressed in mesoderm including muscles, heart, or lymph glands (Figure 1 Columm A).…”

Section: Bioinformatics Analysis Of Drosophila Lim Domain Proteinsmentioning

confidence: 99%

“…As a structural protein, such as Mlp84B, is the cytoskeletal protein, directly affects muscle structure and function. From Fly-FISH and FlyExpress (23)(24)(25)(26)(27), we knew that some of LIM domain mRNAs were located in lymph glands, muscles system, and circulatory system, which inferred that LIM domain genes might have roles in cardiac and hematopoietic morphogenesis. It would be attractive to dissect whether it exists a probable LIM code for the cycle of different cell fates in cardiac and hematopoietic tissues, and this hypothesis needs to be better supported in future studies.…”

Section: Perspectivesmentioning

confidence: 99%

The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis

She

Tang

Jiang

et al. 2021

Front. Cardiovasc. Med.

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Drosophila melanogaster has been used as a model organism for study on development and pathophysiology of the heart. LIM domain proteins act as adaptors or scaffolds to promote the assembly of multimeric protein complexes. We found a total of 75 proteins encoded by 36 genes have LIM domain in Drosophila melanogaster by the tools of SMART, FLY-FISH, and FlyExpress, and around 41.7% proteins with LIM domain locate in lymph glands, muscles system, and circulatory system. Furthermore, we summarized functions of different LIM domain proteins in the development and physiology of fly heart and hematopoietic systems. It would be attractive to determine whether it exists a probable “LIM code” for the cycle of different cell fates in cardiac and hematopoietic tissues. Next, we aspired to propose a new research direction that the LIM domain proteins may play an important role in fly cardiac and hematopoietic morphogenesis.

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“…Mobile applications are generally considered to be timely, contextual, and convenient [1]. Many mobile applications have been built to facilitate tasks that would otherwise require a standalone desktop, such as illustrating macromolecular structure, or analysis results of increasingly complex biological information [2]- [6]. Recently, mobile applications have also been developed to act either directly as an endpoint for query services, or using query services as part of their core functionality, shifting computation from the mobile device to a web server [7], [8].…”

mentioning

confidence: 99%

EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

Gopal

et al. 2017

Preprint

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Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone

Abstract: Search "FlyExpress" on the Apple iTunes store.

Cited by 10 publications

References 7 publications

Automated annotation of developmental stages ofDrosophilaembryos in images containing spatial patterns of expression

Automated annotation of developmental stages ofDrosophilaembryos in images containing spatial patterns of expression

The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis

EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

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