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ArrayExpress update—trends in database growth and links to data analysis tools

Gabriella Rustici, Nikolay Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon Ison, Maria Keays, Natalja Kurbatova, James Malone (+14 others)
2012 Nucleic Acids Research  
The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data.  ...  The ArrayExpress Archive of Functional Genomics Data ( is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus  ...  LINKS TO DATA ANALYSIS TOOLS Approximately 50 GB of data are downloaded every day from ArrayExpress, by an average of 1000 different users.  ... 
doi:10.1093/nar/gks1174 pmid:23193272 pmcid:PMC3531147 fatcat:un6k6u4xqfdjpjt6yhdg5lf6de

ArrayExpress update – from bulk to single-cell expression data

Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A Fonseca, Robert Petryszak, Irene Papatheodorou, Ugis Sarkans, Alvis Brazma
2018 Nucleic Acids Research  
To accommodate these trends, we have substantially changed our submission tool Annotare which, along with raw and processed data, collects all metadata necessary to interpret these experiments.  ...  Data submissions will continue unchanged; all existing ArrayExpress data will be incorporated into BioStudies and the existing accession numbers and application programming interfaces will be maintained  ...  ACKNOWLEDGEMENTS The authors would like to thank Juan Antonio Vicziano. FUNDING  ... 
doi:10.1093/nar/gky964 pmid:30357387 pmcid:PMC6323929 fatcat:p2n5pu6dgffvtf3jp5ypftowxu

NCBI GEO: archive for functional genomics data sets—update

Tanya Barrett, Stephen E. Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F. Kim, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Michelle Holko, Andrey Yefanov, Hyeseung Lee (+5 others)
2012 Nucleic Acids Research  
GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data.  ...  The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats.  ...  As a result, GEO now has supporting data and links to almost 20 000 published manuscripts. Together with ArrayExpress (4), data for >1 million samples are currently available in the public domain.  ... 
doi:10.1093/nar/gks1193 pmid:23193258 pmcid:PMC3531084 fatcat:cgkfwr2dlnepfo7si63m45tgeu

GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox

P. Zimmermann
2004 Plant Physiology  
The authors regret that during the revision of this manuscript, the figures were updated to match the latest status of the database, but the list of contributors was not updated accordingly.  ...  In particular, the authors would like to acknowledge Markus Schmid, Jan U.  ...  (relates to environmental factors); J to L, Meta-Analyzer (multiple gene analysis with respect to anatomy, growth stage, and environmental factors); M and N, Database tool for viewing experiment and array  ... 
doi:10.1104/pp.104.046367 pmid:15375207 pmcid:PMC523327 fatcat:gsho55i4sbek5cgqyfbtrvuwpu

Toward a Public Toxicogenomics Capability for Supporting Predictive Toxicology: Survey of Current Resources and Chemical Indexing of Experiments in GEO and ArrayExpress

ClarLynda R. Williams-Devane, Maritja A. Wolf, Ann M. Richard
2009 Toxicological Sciences  
With these chemical-index files, it is possible for the first time to assess the breadth and overlap of chemical study space represented in these databases, and to begin to assess the sufficiency of data  ...  To begin to address these inadequacies, we focus chemical annotation efforts on experimental content contained in the two primary public genomic resources: ArrayExpress and Gene Expression Omnibus.  ...  ACKNOWLEDGMENTS We would like to thank Drs Jennifer Fostel (CEBS), Chihae Yang (FDA Center for Food Safety and Nutrition), David Dix (EPA), and William Ward (EPA) for helpful comments and suggestions in  ... 
doi:10.1093/toxsci/kfp061 pmid:19332651 fatcat:xe3pftgstfhufpemlwnlbgnhda

Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report

E. T. Chan, J. M. Cherry
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We thank Edith Wong and Benjamin Hitz for their assistance in track setup and GBrowse configuration; Gail Binkley and Stuart Miyasato for adding the Genome Map data files to the downloads  ...  work in classifying the literature and their assistance in defining the workflow for the Genome Map data sets.  ...  In addition, any accession numbers and links to external data sources are gathered, along with all supplementary materials and data depositions to external repositories such as EBI's ArrayExpress (17)  ... 
doi:10.1093/database/bar057 pmid:22434826 pmcid:PMC3308148 fatcat:wwzz7etezvho3hd4fpbe4b44ia

The International Nucleotide Sequence Database Collaboration

G. Cochrane, I. Karsch-Mizrachi, Y. Nakamura
2010 Nucleic Acids Research  
Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core  ...  In this article, we introduce the INSDC, outline data growth patterns and comment on the challenges of increased growth.  ...  The sequence read, quality and read alignment data are stored in binary data files and linked to the SRA metadata layer.  ... 
doi:10.1093/nar/gkq1150 pmid:21106499 pmcid:PMC3013722 fatcat:pxrcwpdacjekxar5ukk4qqhugm

arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies

Haoyang Cai, Nitin Kumar, Michael Baudis, Ying Xu
2012 PLoS ONE  
Results from multi-case selections can be connected to downstream data analysis and visualization tools.  ...  The arrayMap database provides a platform for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data.  ...  Author Contributions Conceived and designed the experiments: HC NK MB. Performed the experiments: HC MB. Analyzed the data: HC NK MB. Contributed reagents/materials/analysis tools: HC NK MB.  ... 
doi:10.1371/journal.pone.0036944 pmid:22629346 pmcid:PMC3356349 fatcat:abrwgh37czg77bizy7hrzsk6ku

Gene Expression Atlas at the European Bioinformatics Institute

Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen Parkinson, Alvis Brazma
2009 Nucleic Acids Research  
The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data.  ...  The query results are ranked using various statistical measures and by how many independent studies in the database show the particular gene-condition association.  ...  ACKNOWLEDGEMENTS In addition to the invaluable help from the entire Microarrays Team, we would like to thank especially the work of Richard Coulson, Ekaterina Pilicheva, Niran Abeygunawardena and Ugis  ... 
doi:10.1093/nar/gkp936 pmid:19906730 pmcid:PMC2808905 fatcat:ruisihx4frgvbkwhmun2b6dyoy

Macromolecular Databases – A Background of Bioinformatics

Tibor Toth, Donatella Verbanac, Dubravko Jelić
2003 Food Technology and Biotechnology  
We would like to express our gratitude to the editors of databases for their courtesy and permission to introduce the database logos, pictures, tables and diagrams within this paper.  ...  Acknowledgements Many thanks to Prof. Dr. Ivana Weygand \ura{evi} and Dr. Boris Mildner for their great help and critical assessment of this work.  ...  These tools enable clustering of data and other types of data analysis. B.1.4.15.  ... 
doaj:bbe088d5f4874cb4a5ec2c7432482957 fatcat:dia4wh55inb2dgfp37zco5eg5i

Sharing and Reusing Gene Expression Profiling Data in Neuroscience

Xiang Wan, Paul Pavlidis
2007 Neuroinformatics  
Here we review the public availability of high-throughput expression data in neuroscience and how it has been re-used, and tools that have been developed to facilitate reuse.  ...  There is increasing interest in making expression data re-use a routine part of the neuroscience tool-kit, but there are a number of challenges.  ...  We are indebted to the many groups who generously provide expression data. Supported by NIH GM076990 and a Michael Smith Foundation for Health Research Career Award to P.P.  ... 
doi:10.1007/s12021-007-0012-5 pmid:17917127 pmcid:PMC2980754 fatcat:kh3doe5dyjck3bqrzeo73aggau

INsPeCT: INtegrative Platform for Cancer Transcriptomics

Piyush B. Madhamshettiwar, Stefan R. Maetschke, Melissa J. Davis, Antonio Reverter, Mark A. Ragan
2014 Cancer Informatics  
Computational analysis, integration, and data visualization are now major bottlenecks in cancer biology and translational research.  ...  Although many tools have been brought to bear on these problems, their use remains unnecessarily restricted to computational biologists, as many tools require scripting skills, data infrastructure, and  ...  Acknowledgements We thank Dr Timothy Bailey for valuable advice on implementation of the MEME Suite of tools and CpG detection program; Mr Gavin Graham, Dr Gerald Hartig, and Mr Alex Varlokov from Bioinformatics  ... 
doi:10.4137/cin.s13630 pmid:24653643 pmcid:PMC3956744 fatcat:i6veph3adjfy3kou7owxzf4gve

Gene Expression Databases and Data Mining

Pascale Anderle, Manuel Duval, Sorin Draghici, Alexander Kuklin, Timothy G. Littlejohn, Juan F. Medrano, David Vilanova, Matthew Alan Roberts
2003 BioTechniques  
The workflow is used to reference appropriate databases and tools for each step in the process of array experimentation.  ...  The majority of the initial technical challenges of conducting experiments are being resolved, only to be replaced with new informatics hurdles, including statistical analysis, data visualization, interpretation  ...  In the present example, the database and analysis tools listed in Tables 3 and 4 would be used to scale, normalize, cluster, manipulate, and visualize the global data sets to fairly compare gene expression  ... 
doi:10.2144/mar03anderle fatcat:zpb3h3ngjrcahbxpl4gvd4mpv4

Managing core resources for genomics and proteomics

Rolf Apweiler, Maria Jesus Martin, Claire O'Donovan, Manuela Pruess
2003 Pharmacogenomics (London)  
This trend and the need for computational analyses of the data make databases essential tools for biological research.  ...  Furthermore, it is necessary to provide users with effective tools to search the databases and to analyze the data.  ...  SRS has addressed many of the difficulties in database access, integration of databases, and analysis tools. SRS is an integration system for both data retrieval and data analysis applications.  ... 
doi:10.1517/phgs.4.3.343.22689 pmid:12718724 fatcat:g6vudrj3hvdehj2jokjiusxkcm

Gramene 2016: comparative plant genomics and pathway resources

Marcela K. Tello-Ruiz, Joshua Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule (+20 others)
2015 Nucleic Acids Research  
Since our last NAR update, the database website adopted a new Drupal management platform.  ...  Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants.  ...  Dylan Beorchia, Teague Green and Kindra Amoss (OSU) for their help in pathway curation; Samuel Fox and Matthew Geniza (OSU) on gene expression Atlas curation and data analysis.  ... 
doi:10.1093/nar/gkv1179 pmid:26553803 pmcid:PMC4702844 fatcat:q6fdmpjqxnarxerc6qokt6i6ui
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