dictyNews

Electronic Edition

Volume 43, number 10

May 12, 2017



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Abstracts

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dictyExpress: a Web-Based Platform for Sequence Data Management 

and Analytics in Dictyostelium and Beyond



Miha Stajdohar, Rafael D Rosengarten, Janez Kokosar, Luka Jeran, 

Domen Blenkus, Gad Shaulsky and Blaz Zupan



Genialis Inc., Houston, TX, USA

Baylor College of Medicine, Houston, TX, USA

University of Ljubljana, Ljubljana, Slovenia





BMC Bioinformatics, in press



Background: Dictyostelium discoideum, a soil-dwelling social amoeba, is a

model for the study of numerous biological processes. Research in the field 

has benefited mightily from the adoption of next-generation sequencing for 

genomic sand transcriptomics. Dictyostelium biologists now face the 

widespread challenges of analyzing and exploring high dimensional data 

sets to generate hypotheses and discovering novel insights.



Results: We present dictyExpress (2.0), a web application designed for

exploratory analysis of gene expression data, as well as data from related

experiments such as Chromatin Immunoprecipitation sequencing (ChIP-Seq). 

The application features visualization modules that include time course 

expression profiles, clustering, gene ontology enrichment analysis, differential 

expression analysis and comparison of experiments. All visualizations are 

interactive and interconnected, such that the selection of genes in one 

module propagates instantly to visualizations in other modules. dictyExpress 

currently stores the data from over 800 Dictyostelium experiments and is 

embedded within a general-purpose software framework for management of 

next-generation sequencing data. dictyExpress allows users to explore their 

data in a broader context by reciprocal linking with dictyBase|a repository of 

Dictyostelium genomic data. In addition, we introduce a companion application 

called GenBoard, an intuitive graphic user interface for data management and

bioinformatics analysis.



Conclusions: dictyExpress and GenBoard enable broad adoption of next

generation sequencing based inquiries by the Dictyostelium research community.

Labs without the means to undertake deep sequencing projects can mine the 

data available to the public. The entire information flow, from raw sequence data 

to hypothesis testing, can be accomplished in an efficient workspace. The 

software framework is generalizable and represents a useful approach for any 

research community. To encourage more wide usage, the backend is open-

source, available for extension and further development by bioinformaticians 

and data scientists.





submitted by: Gad Shaulsky [[log in to unmask]]

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Fold-change detection and scale-invariance of cell-cell signaling in social 

amoeba



Keita Kamino, Yohei Kondo, Akihiko Nakajima, Mai Honda-Kitahara, 

Kunihiko Kaneko and Satoshi Sawai



Graduate School of Arts and Sciences, University of Tokyo





PNAS, in press

doi: 10.1073/pnas.1702181114



Cell-cell signaling is subject to variability in the extracellular volume, cell 

number and dilution that potentially increase uncertainty in the absolute 

concentrations of the extracellular signaling molecules.   To direct cell 

aggregation, the social amoebae Dictyostelium discoideum collectively give 

rise to oscillations and waves of cyclic adenosine 3’, 5’- monophosphate 

(cAMP) under a wide range of cell density.  To date, the systems-level 

mechanism underlying the robustness is unclear.  By employing quantitative 

live cell imaging, here we show that the magnitude of the cAMP relay 

response of individual cells is determined by fold-change in the extracellular 

cAMP concentrations.  The range of cell density and exogenous cAMP 

concentrations that support oscillations at the population-level agrees well 

with conditions that support a large fold-change-dependent response at the 

single-cell level.   Mathematical analysis suggests that invariance of the 

oscillations to density transformation is a natural outcome of combining 

secrete-and-sense systems with a fold-change detection mechanism.





submitted by: Satoshi Sawai [[log in to unmask]]

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[End dictyNews, volume 43, number 10]