A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
Filters
ArrayExpress update—trends in database growth and links to data analysis tools
2012
Nucleic Acids Research
Preserved Fulltext
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 (http://www.ebi.ac.uk/arrayexpress) 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
2018
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2012
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2004
Plant Physiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2009
Toxicological Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
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
2012
Database: The Journal of Biological Databases and Curation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2015; you can also visit the original URL.
The file type is application/pdf.
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
2010
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2012
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Other Versions
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
2009
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2003
Food Technology and Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2007
Neuroinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
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
2014
Cancer Informatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2003
BioTechniques
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2005; you can also visit the original URL.
The file type is application/pdf.
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
2003
Pharmacogenomics (London)
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2003; you can also visit the original URL.
The file type is application/pdf.
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
2015
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 273 results