FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

Pisarev, Andrei; Poustelnikova, Ekaterina; Samsonova, Maria; Reinitz, John

doi:10.1093/nar/gkn717

Cited by 127 publications

(150 citation statements)

References 20 publications

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“…Along the anteroposterior axis, the posterior border of HLH54F expression is apparently defined by the posterior expression border of sna, which is delineated by the repressive action from hkb. We propose that the anterior border of HLH54F is determined by near-maximal threshold levels of tll, the expression of which declines steeply in the area anterior to the HLH54F domain (Pisarev et al, 2009). However, tll acts largely indirectly, through the combined activities of its downstream genes byn and fkh, in activating HLH54F (Fig.…”

Section: Discussionmentioning

confidence: 97%

HLH54Fis required for the specification and migration of longitudinal gut muscle founders from the caudal mesoderm ofDrosophila

et al. 2010

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SUMMARYHLH54F, the Drosophila ortholog of the vertebrate basic helix-loop-helix domain-encoding genes capsulin and musculin, is expressed in the founder cells and developing muscle fibers of the longitudinal midgut muscles. These cells descend from the posterior-most portion of the mesoderm, termed the caudal visceral mesoderm (CVM), and migrate onto the trunk visceral mesoderm prior to undergoing myoblast fusion and muscle fiber formation. We show that HLH54F expression in the CVM is regulated by a combination of terminal patterning genes and snail. We generated HLH54F mutations and show that this gene is crucial for the specification, migration and survival of the CVM cells and the longitudinal midgut muscle founders. HLH54F mutant embryos, larvae, and adults lack all longitudinal midgut muscles, which causes defects in gut morphology and integrity. The function of HLH54F as a direct activator of gene expression is exemplified by our analysis of a CVM-specific enhancer from the Dorsocross locus, which requires combined inputs from HLH54F and Biniou in a feed-forward fashion. We conclude that HLH54F is the earliest specific regulator of CVM development and that it plays a pivotal role in all major aspects of development and differentiation of this largely twist-independent population of mesodermal cells.

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Section: Discussionmentioning

confidence: 97%

HLH54Fis required for the specification and migration of longitudinal gut muscle founders from the caudal mesoderm ofDrosophila

et al. 2010

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“…The number of nuclei along the A-P axis is doubled when going from c13 to c14. The model is fitted to data on gap protein concentrations from the FlyEx database (Pisarev et al, 2008) and mRNA concentrations from SuperFly (Cicin-Sain et al, 2015). To fit the model we used the residual sum of squared differences between the model output and data and we used the weighted Pattern Generation Potential proposed in Samee & Sinha (2013) as the second objective function:…”

Section: The Methods Test On Reduced Model Of Gene Regulationmentioning

confidence: 99%

A software for parameter optimization with Differential Evolution Entirely Parallel method

Kozlov

Samsonov

Samsonova

2016

PeerJ Computer Science

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Summary. Differential Evolution Entirely Parallel (DEEP) package is a software for finding unknown real and integer parameters in dynamical models of biological processes by minimizing one or even several objective functions that measure the deviation of model solution from data. Numerical solutions provided by the most efficient global optimization methods are often problem-specific and cannot be easily adapted to other tasks. In contrast, DEEP allows a user to describe both mathematical model and objective function in any programming language, such as R, Octave or Python and others. Being implemented in C, DEEP demonstrates as good performance as the top three methods from CEC-2014 (Competition on evolutionary computation) benchmark and was successfully applied to several biological problems. Availability. DEEP method is an open source and free software distributed under the terms of GPL licence version 3. The sources are available at http://deepmethod. sourceforge.net/ and binary packages for Fedora GNU/Linux are provided for RPM package manager at https://build.opensuse.org/project/repositories/home:mackoel: compbio.

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“…The quantitative bcd gene expression data in wild-type Drosophila melanogaster embryos was obtained from FlyEx database [18]. This dataset has been widely used as a valuable source of information for studying the dynamics of segment determination of early Drosophila development [13].…”

Section: Real Datamentioning

confidence: 99%

Evaluating the analytical distribution of bicoid gene expression profile

Hassani¹,

Ghodsi

2017

Meta Gene

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Segmentation in Drosophila melanogaster starts with a key maternal input known as bicoid gene. The initial positional information provided by this gene induces the sequential activation of segmentation network. Therefore, an accurate mathematical model describing the gene expression profile of bicoid gene expects to provide essential insights into the gene cross-regulations presented in that network. The significantly stochastic, highly volatile and non-normal nature of the bicoid gene expression profile encouraged us to look for the best distribution function describing this profile. We exploit the use of fifty-four different powerful and widely-used distributions and conclude that FatigueLife(3P) fits the data more accurately than the other distributions. The reliability and validity of the results are evaluated via both simulation studies and empirical evidence thereby adding more confidence and value to the findings of this research.

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FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

Cited by 127 publications

References 20 publications

HLH54Fis required for the specification and migration of longitudinal gut muscle founders from the caudal mesoderm ofDrosophila

HLH54Fis required for the specification and migration of longitudinal gut muscle founders from the caudal mesoderm ofDrosophila

A software for parameter optimization with Differential Evolution Entirely Parallel method

Evaluating the analytical distribution of bicoid gene expression profile

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