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BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

S. Durinck, Y. Moreau, A. Kasprzyk, S. Davis, B. De Moor, A. Brazma, W. Huber
2005 Bioinformatics  
The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.  ...  biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g.  ...  ACKNOWLEDGEMENTS The authors would like to thank Ewan Birney for the fruitful discussions on BioMart.  ... 
doi:10.1093/bioinformatics/bti525 pmid:16082012 fatcat:yzjsj3t5ezdp5n4f6ue4fb2fnu

Microarray data mining using Bioconductor packages

Haisheng Nie, Pieter BT Neerincx, Jan Poel, Francesco Ferrari, Silvio Bicciato, Jack AM Leunissen, Martien AM Groenen
2009 BMC Proceedings  
This paper describes the results of a Gene Ontology (GO) term enrichment analysis of chicken microarray data using the Bioconductor packages.  ...  Some of the GO terms linked to, generally, primary immune responses or secondary immune responses indicating the GO enrichment analysis is a useful approach to analyze microarray data.  ...  Annemarie Rebel and colleagues from Animal Sciences Group in Lelystad for providing the microarray data from the chicken infection experiment.  ... 
doi:10.1186/1753-6561-3-s4-s9 pmid:19615122 pmcid:PMC2712752 fatcat:jpcaijzdsjhwzox2gzlv5ymr44

Ensembl BioMarts: a hub for data retrieval across taxonomic space

R. J. Kinsella, A. Kahari, S. Haider, J. Zamora, G. Proctor, G. Spudich, J. Almeida-King, D. Staines, P. Derwent, A. Kerhornou, P. Kersey, P. Flicek
2011 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors thank all the users of the Ensembl and Ensembl Genomes projects especially those who have provided us with feedback about the Ensembl BioMarts.  ...  The authors would also like to thank the members of the BioMart team at the Ontario Institute for Cancer Research (OICR), especially Dr Arek Kasprzyk, for providing sustained technical support and assistance  ...  is a powerful feature of the BioMart tool.  ... 
doi:10.1093/database/bar030 pmid:21785142 pmcid:PMC3170168 fatcat:z67j6neqxjghdepgpjv6znqddm

Orchestrating high-throughput genomic analysis with Bioconductor

Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne (+14 others)
2015 Nature Methods  
Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology.  ...  Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists.  ...  ACKNOWLEDGMENTS We thank all contributors to the Bioconductor and R projects.  ... 
doi:10.1038/nmeth.3252 pmid:25633503 pmcid:PMC4509590 fatcat:crugw7minjdrxjqhjzkw3s7z34

Visualization of proteomics data usingRand Bioconductor

Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
2015 Proteomics  
We present a summary of R's plotting systems and how they are used to visualize and understand raw and processed MS-based proteomics data.  ...  Data visualization plays a key role in high-throughput biology. It is an essential tool for data exploration allowing to shed light on data structure and patterns of interest.  ...  ) as well as infrastructure dedicated to the analysis and visualization of biological data.  ... 
doi:10.1002/pmic.201400392 pmid:25690415 pmcid:PMC4510819 fatcat:rfdvcmeenjcm3i3haesxljy4uq

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'

Alexandre Kuhn, Ruth Luthi-Carter, Mauro Delorenzi
2008 BMC Bioinformatics  
Results: We provide annotationTools, a Bioconductor-compliant R package to annotate microarray experiments and integrate heterogeneous gene expression profiles using annotation and other molecular biology  ...  This common flat database format thus provides a simple and robust solution to flexibly integrate various sources of information and a basis for the combined analysis of heterogeneous gene expression profiles  ...  Another Bioconductor solution is provided by the package biomaRt which allows the (online) query of biomart databases (like e.g. Ensembl).  ... 
doi:10.1186/1471-2105-9-26 pmid:18201381 pmcid:PMC2267709 fatcat:btgfumnp3fgc3l4mplip34goem

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor [article]

Maria Rodrigo-Domingo, Rasmus Waagepetersen, Julie Støve Bødker, Steffen Falgreen, Malene Krag Kjeldsen, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted
2013 arXiv   pre-print
Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large variety of pre-processing and filtering steps employed before the actual analysis  ...  We here give a detailed workflow on how to perform reproducible analysis of the GeneChip Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their simplicity  ...  All authors read and approved the final manuscript. [7] R Development Core Team . R: A Language and Environment for Statistical Computing.  ... 
arXiv:1302.3790v2 fatcat:zsfekoydbfamxbawwb5kggzv64

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor

M. Rodrigo-Domingo, R. Waagepetersen, J. S. Bodker, S. Falgreen, M. K. Kjeldsen, H. E. Johnsen, K. Dybkaer, M. Bogsted
2013 Briefings in Bioinformatics  
Reproducing results from published microarray data represents a challenge owing to the vast amounts of data and the large variety of preprocessing and filtering steps used before the actual analysis is  ...  We here give a detailed workflow on how to perform reproducible analysis of the GeneChip Õ Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their  ...  The research is supported by MSCNET, a translational program studying cancer stem cells in multiple myeloma supported by the EU FP6, and CHEPRE, a program studying chemo sensitivity in malignant lymphoma  ... 
doi:10.1093/bib/bbt011 pmid:23603090 pmcid:PMC4103539 fatcat:tsxmdaezjjb7rktbqturv5sfha

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis

Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
2015 BMC Bioinformatics  
In genome-wide studies, over-representation analysis (ORA) against a set of genes is an essential step for biological interpretation.  ...  By utilizing the enriched MeSH terms, related PubMed documents can be retrieved and saved on local machines within this framework.  ...  We also thank Margaret McGhee and Veronica Robinson Garrett for providing the licensed PubMed data.  ... 
doi:10.1186/s12859-015-0453-z pmid:25887539 pmcid:PMC4343279 fatcat:4mnp7rqmkrgm5dvlcdtqchkk3m

BioMart – biological queries made easy

Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk
2009 BMC Genomics  
Frequently, more than one data source is required and for high-throughput analysis, cutting and pasting results between websites is certainly very time consuming.  ...  BioMart enables scientists to perform advanced querying of biological data sources through a single web interface.  ...  Acknowledgements We thank the Wellcome Trust, EMBL and the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology for health", contract number  ... 
doi:10.1186/1471-2164-10-22 pmid:19144180 pmcid:PMC2649164 fatcat:cn2znm3jdjbfrimhmkgulgfjbe

Online resources of cancer data: barriers, benefits and lessons

E. Gadaleta, N. R. Lemoine, C. Chelala
2010 Briefings in Bioinformatics  
However, a key factor in the utility, sustainability and future use of a novel resource lies in its ability to allow for data sharing and to be interoperable with major international cancer research efforts  ...  This article will introduce some of these efforts, the interoperable cancer data-mining resources and repositories, from a user-perspective.  ...  For instance, Reactome is a repository of biological pathways and reactions available as a BioMart database [68] .  ... 
doi:10.1093/bib/bbq010 pmid:20348133 fatcat:tinslegov5hyxnx44bm2qvz6ua

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic B. Bastian
2016 F1000Research  
BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database.  ...  This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags  ...  Conclusion In summary, the BgeeDB package serves as a bridge between data from the Bgee database and the R/Bioconductor environment, facilitating access to high-quality curated and re-analyzed gene expression  ... 
doi:10.12688/f1000research.9973.1 pmid:30467516 pmcid:PMC6113886 fatcat:to7kalgjwvah3mvudjv3u4suzm

Solutions for data integration in functional genomics: a critical assessment and case study

D. Smedley, M. A. Swertz, K. Wolstencroft, G. Proctor, M. Zouberakis, J. Bard, J. M. Hancock, P. Schofield
2008 Briefings in Bioinformatics  
with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases.  ...  We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval.  ...  This makes it possible to feed the results of a BioMart query into the powerful statistical and analytical tools that R and BioConductor provide.  ... 
doi:10.1093/bib/bbn040 pmid:19112082 fatcat:6hoxfuktznhkbcfemik2rb4jqq

Towards dynamic database infrastructures for mouse genetics

Morris A. Swertz, Damian Smedley, Katy Wolstencroft, Rudi Alberts, Michael Zouberakis, Vassilis Aidinis, Klaus Schughart, Paul N. Schofield, Ritsert C. Jansen
2008 2008 8th IEEE International Conference on BioInformatics and BioEngineering  
Combined analysis of these datasets provides much of the power of the approach of functional genomics but this depends on the ability of databases to exchange data with each other and with analytical software  ...  We here report on two pilot projects and distill preliminary recommendations.  ...  The workflow model is a record of such integration procedure describing what data sources have been linked and what 'shims' have been added for data conversion between them.  ... 
doi:10.1109/bibe.2008.4696715 dblp:conf/bibe/SwertzSWAZASSJ08 fatcat:5poa5rcyqbbpxjcvzk2wmq3ixa

Genome data mining for everyone

Gir-Won Lee, Sang-Soo Kim
2008 BMB Reports  
Intelligent use of the data should expedite biological knowledge discovery. Such activity is collectively called data mining and involves queries that can be simple, complex, and even combinational.  ...  Typically, these genome sequences and the associated annotation data are accessed through Internet-based genome browsers that offer a user-friendly interface.  ...  A recently introduced R module known as biomaRt (26) enables direct access to Ensembl BioMart databases (24) from the statistical package R and its bio-data analysis environment, Bioconductor (19) .  ... 
doi:10.5483/bmbrep.2008.41.11.757 pmid:19017486 fatcat:wyqjvp2xtjfvrp4idajl4yntay
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