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BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments

Arianna Consiglio, Massimo Carella, Giorgio De Caro, Gianfranco Delle Foglie, Candida Giovannelli, Giorgio Grillo, Massimo Ianigro, Flavio Licciulli, Orazio Palumbo, Ada Piepoli, Elena Ranieri, Sabino Liuni
2012 BMC Bioinformatics  
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

Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano
2008 BMC Bioinformatics  
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

Pascal Gellert, Yuliya Ponomareva, Thomas Braun, Shizuka Uchida
2012 Nucleic Acids Research  
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

Michał J Okoniewski, Tim Yates, Siân Dibben, Crispin J Miller
2007 Genome Biology  
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

Ting-Yu Chang, Yin-Yi Li, Chih-Hung Jen, Tsun-Po Yang, Chi-Hung Lin, Ming-Ta Hsu, Hsei-Wei Wang
2008 BMC Bioinformatics  
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

Ping Chen, Tatiana Lepikhova, Yizhou Hu, Outi Monni, Sampsa Hautaniemi
2011 Nucleic Acids Research  
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

Dorothea Emig, Nathan Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, Mario Albrecht
2010 Nucleic Acids Research  
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

A. Koschmieder, K. Zimmermann, S. Trissl, T. Stoltmann, U. Leser
2011 Briefings in Bioinformatics  
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

F. Birzele, R. Kuffner, F. Meier, F. Oefinger, C. Potthast, R. Zimmer
2007 Nucleic Acids Research  
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

Pascal Gellert, Mizue Teranishi, Katharina Jenniches, Piera De Gaspari, David John, Karsten grosse Kreymborg, Thomas Braun, Shizuka Uchida
2011 Nucleic Acids Research  
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) (, 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

R. Sanges, F. Cordero, R. A. Calogero
2007 Bioinformatics  
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

Alberto Risueño, Celia Fontanillo, Marcel E Dinger, Javier De Las Rivas
2010 BMC Bioinformatics  
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

G Barton, J Abbott, N Chiba, DW Huang, Y Huang, M Krznaric, J Mack-Smith, A Saleem, BT Sherman, B Tiwari, C Tomlinson, T Aitman (+4 others)
2008 BMC Bioinformatics  
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

Hongkai Ji, Hui Jiang, Wenxiu Ma, David S Johnson, Richard M Myers, Wing H Wong
2008 Nature Biotechnology  
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

Dajie Luo
2012 The Open Bioinformatics Journal  
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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