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UPSC-BASE: Populus transcriptomics online
Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
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2006 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 48, no 5, 806-817 p.Article in journal (Refereed) Published
Abstract [en]

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.

 

Place, publisher, year, edition, pages
Oxford: Blackwell , 2006. Vol. 48, no 5, 806-817 p.
Keyword [en]
Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Plant, Internet, Populus/*genetics
Identifiers
URN: urn:nbn:se:umu:diva-2741DOI: 10.1111/j.1365-313X.2006.02920.xOAI: oai:DiVA.org:umu-2741DiVA: diva2:140998
Available from: 2007-11-07 Created: 2007-11-07 Last updated: 2017-12-14Bibliographically approved
In thesis
1. Populus transcriptomics: from noise to biology
Open this publication in new window or tab >>Populus transcriptomics: from noise to biology
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [sv]

Mikromatriser handlar numera inte bara om att alstra genuttrycksdata i snabb takt, utan det är minst lika viktigt att effektivt ta hand om informationen efteråt. I den här avhandlingen presenteras ett arbetsflöde för att mäta, lagra och analysera genuttrycksdata i asp och poppel (Populus spp.). En Populus} mikromatrisdatabas - UPSC--BASE - tillgänglig för alla intresserade, utvecklades i syfte att samla in och lagra genuttrycksdata. Flertalet analysverktyg gjordes samtidigt tillgängliga, för att möjliggöra ett smidigt arbetsflöde från rådata till biologiska slutsatser.

En av de stora utmaningarna i analys av mikromatriser är att kunna särskilja bruset från värdefull biologisk information. Att studera träd som växer utomhus är komplext eftersom de interagerar med omgivningen i mycket större utsträckning än vad som är fallet i växthusets kontrollerade miljö. Det här arbetet visar att det är möjligt, med hjälp av avancerad statistik och god försöksplanering, att följa och jämföra genuttrycket i blad från aspar utomhus under flera år för att dra värdefulla slutsatser om geners reglering.

Den lagrade biologiska informationen i UPSC-BASE är avsedd att vara en värdefull tillgång för växtfältet i stort. I databasen finns nästan hundra olika experiment som innefattar alltifrån unga blad till ved, insektsangrepp, kyla och torka samt studier av genmodifierade växter. Informationen kan användas både för jämförande studier inom olika aspförsök, men också för att jämföra med andra växter. För att illustrera möjligheterna, studerades och grupperades gener i blad baserat på hur de uppträder över alla dessa experiment. Dessa grupperingar användes sedan för att definiera gener som är viktiga i bladutvecklingen. Sammanfattningsvis ger arbetet som presenteras i denna avhandling tillgång till verktyg och kunskap för storskaliga studier av genuttryck och den lagrade informationen har bevisats vara en värdefull tillgång för mer ingående studier av geners reglering.

Abstract [en]

DNA microarray analysis today is not just generation of high-throughput data, much more attention is paid to the subsequent efficient handling of the generated information. In this thesis, a pipeline to generate, store and analyse Populus transcriptional data is presented A public Populus microarray database - UPSC--BASE - was developed to gather and store transcriptomic data. In addition, several tools were provided to facilitate microarray analysis without requirements for expert-level knowledge. The aim has been to streamline the workflow from raw data through to biological interpretation.

Differentiating noise from valuable biological information is one of the challenges in DNA microarray analysis. Studying gene regulation in free-growing aspen trees represents a complex analysis scenario as the trees are exposed to, and interacting with, the environment to a much higher extent than under highly controlled conditions in the greenhouse. This work shows that, by using multivariate statistics and experimental planning, it is possible to follow and compare gene expression in leaves from multiple growing seasons, and draw valuable conclusions about gene expression from field-grown samples.

The biological information in UPSC-BASE is intended to be a valuable transcriptomic resource also for the wider plant community. The database provides information from almost a hundred different experiments, spanning different developmental stages, tissue types, abiotic and biotic stresses and mutants. The information can potentially be used for both cross-experiment analysis and for comparisons against other plants, such as Arabidopsis or rice. As a demonstration of this, microarray experiments performed on Populus leaves were merged and genes preferentially expressed in leaves were organised in to regulons of co-regulated genes. Those regulons were used to define genes of importance in leaf development in Populus. Taken together, the work presented in this thesis provides tools and knowledge for large-scale transcriptional studies and the stored gene expression information has been proven to be a valuable information resource for in-depth studies about gene regulation.

Place, publisher, year, edition, pages
Umeå: Fysiologisk botanik, 2007. 50 p.
Keyword
Populus, microarray, transcriptomics, UPSC-BASE, leaf development
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:umu:diva-1423 (URN)978-91-7264-442-7 (ISBN)
Public defence
2007-11-30, Hörsal, Arbetslivsinstitutet, Umeå universitet, 10:00 (English)
Opponent
Supervisors
Available from: 2007-11-07 Created: 2007-11-07 Last updated: 2009-12-03Bibliographically approved

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Publisher's full texthttp://dx.doi.org/10.1111/j.1365-313X.2006.02920.x

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