ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

Parkinson, Helen; Sarkans, Ugis; Kolesnikov, N. N.; Abeygunawardena, Niran; Burdett, Tony; Dylag, Miroslaw; Emam, Ibrahim; Farne, Anna; Hastings, Emma; Holloway, Ele; Kurbatova, Natalja; Lukk, Margus; Malone, James; Mani, Roby; Pilicheva, Ekaterina; Rustici, Gabriella; Sharma, Ashish; Williams, Eleanor; Adamusiak, Tomasz; Brandizi, Marco; Sklyar, Nataliya; Brāzma, Alvis

doi:10.1093/nar/gkq1040

Cited by 289 publications

(247 citation statements)

References 10 publications

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“…Raw data from the microarray experiments, described in compliance with MIAME (Minimum Information About Microarray Experiment; Brazma et al 2001) guidelines, have been deposited at the ArrayExpress database (http:// www.ebi.ac.uk/arrayexpress, Parkinson et al 2010) under experiment accession numbers E-MEXP-3212 (24 °C/22 °C samples only) and E-MTAB-1252 (24 °C/22 °C and 8 °C/6 °C samples). We have previously documented excellent correspondence of the microarray data with RNA quantitation obtained by RT-qPCR (Trzcinska-Danielewicz et al 2009;Sobkowiak et al 2014Sobkowiak et al , 2016.…”

Section: Data Preprocessing and Statistical Analysismentioning

confidence: 99%

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Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Jończyk

Sobkowiak

Trzcińska-Danielewicz

et al. 2017

Plant Mol Biol

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numerous genes lacking circadian rhythm responded to the cold by undergoing up-or down-regulation. Notably, the transcriptome changes preceded major physiological manifestations of cold stress. In silico analysis of metabolic processes likely affected by observed gene expression changes indicated major down-regulation of photosynthesis, profound and multifarious modulation of plant hormone levels, and of chromatin structure, transcription, and translation. A role of trehalose and stachyose in cold stress signaling was also suggested. Meta-analysis of published transcriptomic data allowed discrimination between general stress response of maize and that unique to severe cold. Several cis-and trans-factors likely involved in the latter were predicted, albeit none of them seemed to have a major role. These results underscore a key role of modulation of diel gene expression in maize response to severe cold and the unique character of the cold-response of the maize circadian clock.

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Section: Data Preprocessing and Statistical Analysismentioning

confidence: 99%

“…To identify transcriptomic changes specific to severe cold we analyzed data deposited in ArrayExpress (Parkinson et al 2010) and Gene Expression Omnibus (Barrett et al 2010) databases. We chose projects on maize responses to stress meeting the following criteria:…”

Section: Meta-analysis Of Transcriptomic Data On Maize Responses To Dmentioning

confidence: 99%

Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Jończyk

Sobkowiak

Trzcińska-Danielewicz

et al. 2017

Plant Mol Biol

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“…We collected 307 GeneChips from publicly available databases including GEO, ArrayExpress (Parkinson et al, 2011), and TFGD (Fei et al, 2011) and included 20 of our own hybridizations (GEO accession no. GSE35020), resulting in a total of 327 arrays.…”

Section: Data Collection and Preprocessingmentioning

confidence: 99%

Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches

Fukushima

Nishizawa²,

Hayakumo³

et al. 2012

Plant Physiology

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Gene-to-gene coexpression analysis provides fundamental information and is a promising approach for predicting unknown gene functions in plants. We investigated various associations in the gene expression of tomato (Solanum lycopersicum) to predict unknown gene functions in an unbiased manner. We obtained more than 300 microarrays from publicly available databases and our own hybridizations, and here, we present tomato coexpression networks and coexpression modules. The topological characteristics of the networks were highly heterogenous. We extracted 465 total coexpression modules from the data set by graph clustering, which allows users to divide a graph effectively into a set of clusters. Of these, 88% were assigned systematically by Gene Ontology terms. Our approaches revealed functional modules in the tomato transcriptome data; the predominant functions of coexpression modules were biologically relevant. We also investigated differential coexpression among data sets consisting of leaf, fruit, and root samples to gain further insights into the tomato transcriptome. We now demonstrate that (1) duplicated genes, as well as metabolic genes, exhibit a small but significant number of differential coexpressions, and (2) a reversal of gene coexpression occurred in two metabolic pathways involved in lycopene and flavonoid biosynthesis. Independent experimental verification of the findings for six selected genes was done using quantitative real-time polymerase chain reaction. Our findings suggest that differential coexpression may assist in the investigation of key regulatory steps in metabolic pathways. The approaches and results reported here will be useful to prioritize candidate genes for further functional genomics studies of tomato metabolism.

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“…They have decided to use the mouse as a model organism and have carried out a variety of transcriptomics and proteomics experiments whose results have been deposited in local copies of, resp., Array Express [57], a database of gene expression and other microarray data, and Pride [65], a standards-compliant repository for proteomics data. In order to support the analysis of the data they obtained, various databases need to be integrated.…”

Section: A Bioinformatics Use Casementioning

confidence: 99%

A Functional Model for Dataspace Management Systems

Hedeler

Fernandes

Belhajjame

et al. 2013

Advanced Query Processing

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Dataspace management systems (DSMSs) hold the promise of pay-asyou-go data integration. We describe a comprehensive model of DSMS functionality using an algebraic style. We begin by characterizing a dataspace life cycle and highlighting opportunities for both automation and user-driven improvement techniques. Building on the observation that many of the techniques developed in model management are of use in data integration contexts as well, we briefly introduce the model management area and explain how previous work on both data integration and model management needs extending if the full dataspace life cycle is to be supported. We show that many model management operators already enable important functionality (e.g., the merging of schemas, the composition of mappings, etc.) and formulate these capabilities in an algebraic structure, thereby giving rise to the notion of the core functionality of a DSMS as a many-sorted algebra. Given this view, we show how core tasks in the dataspace life cycle can be enacted by means of algebraic programs. An extended case study illustrates how such algebraic programs capture a challenging, practical scenario.

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ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

Cited by 289 publications

References 10 publications

Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches

A Functional Model for Dataspace Management Systems

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