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An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
Michał J Okoniewski, Tim Yates, Siân Dibben, Crispin J Miller
Genome Biol. 2007; 8(5): R79. Published online 2007 May 11. doi: 10.1186/gb-2007-8-5-r79
PMCID:
PMC1929135
Abstract Full Text PDF–594K Supplementary Material
 Is Cited by the Following 20 Articles in this Archive:
rnaSeqMap: a Bioconductor package for RNA sequencing data exploration
Anna Leśniewska, Michał J Okoniewski
BMC Bioinformatics. 2011; 12: 200. Published online 2011 May 25. doi: 10.1186/1471-2105-12-200
PMCID:
PMC3128033
Abstract Full Text PDF–854K Supplementary Material
Exon array data analysis using Affymetrix power tools and R statistical software
Helen E. Lockstone
Brief Bioinform. 2011 November; 12(6): 634–644. Published online 2011 April 15. doi: 10.1093/bib/bbq086
PMCID:
PMC3220870
Abstract Full Text PDF–177K
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays
Johannes Eichner, Georg Zeller, Sascha Laubinger, Gunnar Rätsch
BMC Bioinformatics. 2011; 12: 55. Published online 2011 February 16. doi: 10.1186/1471-2105-12-55
PMCID:
PMC3051901
Abstract Full Text PDF–792K Supplementary Material
Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer
Wolfram Langer, Florian Sohler, Gabriele Leder, Georg Beckmann, Henrik Seidel, Jörn Gröne, Michael Hummel, Anette Sommer
BMC Genomics. 2010; 11: 676. Published online 2010 November 30. doi: 10.1186/1471-2164-11-676
PMCID:
PMC3053589
Abstract Full Text PDF–1.0M Supplementary Material
A B2 SINE insertion in the Comt1 gene (Comt1B2i) results in an overexpressing, behavior modifying allele present in classical inbred mouse strains
R L Kember, C Fernandes, E M Tunbridge, L Liu, J L Payá-Cano, M J Parsons, L C Schalkwyk
Genes Brain Behav. 2010 November; 9(8): 925–932. doi: 10.1111/j.1601-183X.2010.00614.x
PMCID:
PMC3037563
Abstract Full Text PDF–1.2M
mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance
Peter A. C. 't Hoen, Michael Hirsch, Emile J. de Meijer, Renée X. de Menezes, Gert Jan van Ommen, Johan T. den Dunnen
Nucleic Acids Res. 2011 January; 39(2): 556–566. Published online 2010 September 17. doi: 10.1093/nar/gkq790
PMCID:
PMC3025562
Abstract Full Text PDF–581K Supplementary Material
The Comparison of Different Pre- and Post-Analysis Filters for Determination of Exon-Level Alternative Splicing Events Using Affymetrix Arrays
Toni Whistler, Cheng-Feng Chiang, Jin-Mann Lin, William Lonergan, William C. Reeves
J Biomol Tech. 2010 April; 21(1): 44–53.
PMCID:
PMC2841991
Abstract Full Text PDF–700K Supplementary Material
An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome
Danny A. Bitton, Duncan L. Smith, Yvonne Connolly, Paul J. Scutt, Crispin J. Miller
PLoS One. 2010; 5(1): e8949. Published online 2010 January 28. doi: 10.1371/journal.pone.0008949
PMCID:
PMC2812506
Abstract Full Text PDF–378K Supplementary Material
Exon Array Analysis of Head and Neck Cancers Identifies a Hypoxia Related Splice Variant of LAMA3 Associated with a Poor Prognosis
Carla S. Moller-Levet, Guy N. J. Betts, Adrian L. Harris, Jarrod J. Homer, Catharine M. L. West, Crispin J. Miller
PLoS Comput Biol. 2009 November; 5(11): e1000571. Published online 2009 November 20. doi: 10.1371/journal.pcbi.1000571
PMCID:
PMC2773424
Abstract Full Text PDF–1004K Supplementary Material
Genome-Wide Analysis of Immune Activation in Human T and B Cells Reveals Distinct Classes of Alternatively Spliced Genes
Yevgeniy A. Grigoryev, Sunil M. Kurian, Aleksey A. Nakorchevskiy, John P. Burke, Daniel Campbell, Steve R. Head, Jun Deng, Aaron B. Kantor, John R. Yates, III, Daniel R. Salomon
PLoS One. 2009; 4(11): e7906. Published online 2009 November 19. doi: 10.1371/journal.pone.0007906
PMCID:
PMC2775942
Abstract Full Text PDF–943K Supplementary Material
Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation
Kevin CH Ha, Jasmin Coulombe-Huntington, Jacek Majewski
BMC Genomics. 2009; 10: 519. Published online 2009 November 12. doi: 10.1186/1471-2164-10-519
PMCID:
PMC2780461
Abstract Full Text PDF–1.3M Supplementary Material
Identifying differential exon splicing using linear models and correlation coefficients
Sonia H Shah, Jacqueline A Pallas
BMC Bioinformatics. 2009; 10: 26. Published online 2009 January 20. doi: 10.1186/1471-2105-10-26
PMCID:
PMC2636774
Abstract Full Text PDF–550K Supplementary Material
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics
Kyongyong Jung, Jongsun Park, Jaeyoung Choi, Bongsoo Park, Seungill Kim, Kyohun Ahn, Jaehyuk Choi, Doil Choi, Seogchan Kang, Yong-Hwan Lee
BMC Genomics. 2008; 9: 586. Published online 2008 December 4. doi: 10.1186/1471-2164-9-586
PMCID:
PMC2649115
Abstract Full Text PDF–1.9M
ExonMiner: Web service for analysis of GeneChip Exon array data
Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano
BMC Bioinformatics. 2008; 9: 494. Published online 2008 November 26. doi: 10.1186/1471-2105-9-494
PMCID:
PMC2621370
Abstract Full Text PDF–1.5M
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, J Darlington, L Game, MJE Sternberg, SA Butcher
BMC Bioinformatics. 2008; 9: 493. Published online 2008 November 25. doi: 10.1186/1471-2105-9-493
PMCID:
PMC2615452
Abstract Full Text PDF–1.5M
Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays
Amandine Bemmo, David Benovoy, Tony Kwan, Daniel J Gaffney, Roderick V Jensen, Jacek Majewski
BMC Genomics. 2008; 9: 529. Published online 2008 November 7. doi: 10.1186/1471-2164-9-529
Correction in:
BMC Genomics. 2009; 10: 121.
PMCID:
PMC2585104
Abstract Full Text PDF–1.6M Supplementary Material Correction
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
BMC Bioinformatics. 2008; 9: 432. Published online 2008 October 14. doi: 10.1186/1471-2105-9-432
PMCID:
PMC2579307
Abstract Full Text PDF–884K
Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor
Michał J Okoniewski, Crispin J Miller
PLoS Comput Biol. 2008 February; 4(2): e6. Published online 2008 February 29. doi: 10.1371/journal.pcbi.0040006
PMCID:
PMC2323405
Full Text PDF–272K Supplementary Material
Exon level integration of proteomics and microarray data
Danny A Bitton, Michał J Okoniewski, Yvonne Connolly, Crispin J Miller
BMC Bioinformatics. 2008; 9: 118. Published online 2008 February 25. doi: 10.1186/1471-2105-9-118
PMCID:
PMC2267708
Abstract Full Text PDF–1.3M
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis
Tim Yates, Michał J. Okoniewski, Crispin J. Miller
Nucleic Acids Res. 2008 January; 36(Database issue): D780–D786. Published online 2008 January. doi: 10.1093/nar/gkm779
PMCID:
PMC2238884
Abstract Full Text PDF–897K
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