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BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments
2012
BMC Bioinformatics
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Results: BEAT is a web tool which allows uploading and analyzing exon array datasets using standard statistical methods and an easy-to-use graphical web front-end. ...
Last generation Affymetrix GeneChip Human Exon 1.0 ST Arrays offer a more detailed view of the gene expression profile providing information on the AS patterns. ...
We would like to thank Ernesto Picardi for his helpful comments and discussions about exon array statistical analysis, Nicola Losito for helping us with servers and data base management, Raffaella Stallone ...
doi:10.1186/1471-2105-13-s4-s21
pmid:22536968
pmcid:PMC3314565
fatcat:vxfvkhavozh5bfcoemasocgdha
ExonMiner: Web service for analysis of GeneChip Exon array data
2008
BMC Bioinformatics
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Results: We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g ...
We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations ...
The authors also wish to thank the Affimetrix Japan Inc. for their allowance to link to their web site: NetAffx, and for their helpful suggestions. ...
doi:10.1186/1471-2105-9-494
pmid:19036125
pmcid:PMC2621370
fatcat:u2hndmrtjrfjfgfcajn7i2t4ce
Noncoder: a web interface for exon array-based detection of long non-coding RNAs
2012
Nucleic Acids Research
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To allow for a general usage to the research community, we developed a user-friendly web interface called 'noncoder'. ...
The web interface is available at ...
ACKNOWLEDGEMENTS The authors thank Dr Jose Clemente for his valuable advice and comments on this article. ...
doi:10.1093/nar/gks877
pmid:23012263
pmcid:PMC3592461
fatcat:jnj22774zrelzh5wqwklvskrii
An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
2007
Genome Biology
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Affymetrix exon arrays contain probesets intended to target every known and predicted exon in the entire genome, posing significant challenges for high-throughput genome-wide data analysis. ...
of exon array data. ...
Rob Clarke provided RNA samples for hybridization, Stuart Pepper, Yvonne Hey and Gillian Newton processed the microarrays and took part in some informative discussions, and Laura Edwards helped with testing ...
doi:10.1186/gb-2007-8-5-r79
pmid:17498294
pmcid:PMC1929135
fatcat:4t6gxo3yajfvpogupinpsyavkq
easyExon – A Java-based GUI tool for processing and visualization of Affymetrix exon array data
2008
BMC Bioinformatics
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Conclusion: EasyExon can efficiently process and analyze the Affymetrix exon array data. ...
The possibility to study alternative splicing (AS) events on a genomic scale using splicing-sensitive microarrays, including the Affymetrix GeneChip Exon 1.0 ST microarray (exon array), has appeared very ...
Availability and requirements Figure 2 2 An easyExon pipeline for analyzing exon array data. (A)Step 1-1, the data input interface. ...
doi:10.1186/1471-2105-9-432
pmid:18851762
pmcid:PMC2579307
fatcat:dbjqs4flyfbdvh3mlqtzcvyiha
Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants
2011
Nucleic Acids Research
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We introduce a novel, computationally efficient methodology, Multiple Exon Array Preprocessing (MEAP), for exon array data pre-processing, analysis and visualization. ...
Analysis of exon array data is more challenging than the analysis of gene expression data and there is a need for reliable quantification of exons and alternatively spliced variants. ...
ACKNOWLEDGEMENTS We thank Riku Louhimo for the integration study on CGH array and exon array HNSCC data, Javier Nu´n˜ez-Fontarnau, Ville Rantanen for helping with parallel implementation and memory recording ...
doi:10.1093/nar/gkr513
pmid:21745820
pmcid:PMC3185423
fatcat:fn25pdszljbb3gxvav5lm3pfcm
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
2010
Nucleic Acids Research
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Both programs provide an intuitive and comprehensive end-to-end solution for the analysis and visualization of alternative splicing data from Affymetrix Exon and Gene Arrays at the level of proteins, domains ...
Our software tools include easy-to-use graphical user interfaces, rigorous statistical methods (FIRMA, MiDAS and DABG filtering) and do not require prior knowledge of exon array analysis or programming ...
Cline and Gary Howard for their valuable advice on the development of AltAnalyze and DomainGraph, and on the article. ...
doi:10.1093/nar/gkq405
pmid:20513647
pmcid:PMC2896198
fatcat:ehwgu6jxpfgvnouesxqgkmottu
Tools for managing and analyzing microarray data
2011
Briefings in Bioinformatics
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The microarray-based analysis of gene expression has become a workhorse for biomedical research. ...
In consequence, choosing the right tool for a given project is difficult even for the expert. ...
We already now want to apologize for any errors in our evaluation. ...
doi:10.1093/bib/bbr010
pmid:21422065
fatcat:3dlnv3hlwbdr3p63aksmpy2iuq
ProSAS: a database for analyzing alternative splicing in the context of protein structures
2007
Nucleic Acids Research
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a structure-based analysis of alternative splicing events. ...
Alternative isoforms annotated in Ensembl or SwissProt can be analyzed on the protein structure and protein function level using an intuitive user interface that provides several features and tools for ...
ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for the article was provided by Ludwig-Maximilians-Universita¨t (LMU) Mu¨nchen. ...
doi:10.1093/nar/gkm793
pmid:17933774
pmcid:PMC2238869
fatcat:lz5wrexf65a65jczk7shorxdwa
Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events
2011
Nucleic Acids Research
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Here, we show that the newly developed Gene Array Analyzer (GAA), which evolved from our previously published Exon Array Analyzer (EAA), enables economic and user-friendly analysis of alternative splicing ...
Exon arrays are regularly used to analyze differential splicing events. ...
In a previous study, we introduced the Exon Array Analyzer (EAA) (http://EAA.mpi-bn.mpg.de), an easy-to-use web tool for analyzing exon arrays for differential expressed exons (10) . ...
doi:10.1093/nar/gkr1110
pmid:22123740
pmcid:PMC3315316
fatcat:bqkuamjg5vfsfnzbnsfr6s3xcu
oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language
2007
Bioinformatics
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Affymetrix 3 0 expression (IVT) arrays as well as the new whole transcript expression arrays, i.e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI is available for most platforms on which R runs ...
This library provides a graphical interface (GUI) for Bioconductor libraries to be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays ...
For exon arrays, a filter based on DABG P-values is also available. ...
doi:10.1093/bioinformatics/btm469
pmid:17875544
fatcat:64tpxnkonfcrhiy7gj4r6g46ae
GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
2010
BMC Bioinformatics
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In the case of all-exon arrays, this provides a means by which the expression of the individual exons within a gene can be compared, thereby facilitating the identification and analysis of alternatively ...
The application integrates data from four major source databases: Ensembl, RNAdb, Affymetrix and GeneAtlas; and it provides the users with a series of files and packages (R CDFs) to analyze particular ...
Author Details 1 Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca, Spain and 2 Institute for Molecular Bioscience, University of Queensland ...
doi:10.1186/1471-2105-11-221
pmid:20429936
pmcid:PMC2875241
fatcat:bejkvf2hzbg4rf6u4pyrs73gpi
EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management
2008
BMC Bioinformatics
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EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. ...
steps, all through a single easy to use web portal. ...
Abbreviations Steven Newhouse (currently at Microsoft, Redmond WA) and Helen Causton for helpful technical input during the initial project phase. ...
doi:10.1186/1471-2105-9-493
pmid:19032776
pmcid:PMC2615452
fatcat:a4o62r7glbhl7jgerxhprkhrcm
An integrated software system for analyzing ChIP-chip and ChIP-seq data
2008
Nature Biotechnology
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We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. ...
We demonstrate the use of these tools by a comparative analysis of ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST, a study of ChIP-seq analysis with or without a negative control sample ...
Li for assistance with analyzing the ChIP-chip spike-in data. ...
doi:10.1038/nbt.1505
pmid:18978777
pmcid:PMC2596672
fatcat:jvro3fijl5e7jfy2lgkulc3ju4
A Cloud Computing System to Quickly Implement New Microarray Data Pre-processing Methods
2012
The Open Bioinformatics Journal
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More importantly, R packages, e. g., for newly-developed normalization methods, and GC-robust multichip algorithm (RMA) for exon arrays, can be easily incorporated into the system with limited inputs from ...
Users can access the application with a newly incorporated module through the Web. ...
Chen for proof reading. The project is partially support by a CO-BRE grant from NCRR, NIH to D. Luo, P. Banerjee and Institutional funding from WVU CTSI. ...
doi:10.2174/1875036201206010037
fatcat:7g5g4y5elncrhco575vbbbfn6q
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