ExonMiner: Web service for analysis of GeneChip Exon array data

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Numata, Kazuyuki ^a   Yoshida, Ryo ^b   Nagasaki, Masao ^a   Saito, Ayumu ^a   Imoto, Seiya ^a   Miyano, Satoru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DATA NORMALIZATION; EXPRESSION PROFILE; INTERNET BROWSERS; MASSIVE DATA SETS; META-ANALYSIS; SPLICE VARIANTS; TRANSCRIPTIONAL REGULATION; TWO-WAY ANOVA;

CELLS; GENES; PERSONAL COMPUTERS; STATISTICAL METHODS; SUPERCOMPUTERS; WEB SERVICES; WEBSITES;

DATA VISUALIZATION;

ISOPROTEIN;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; DNA MICROARRAY; EXON; GENE EXPRESSION PROFILING; GENETICS; INTERNET; METHODOLOGY;

COMPUTATIONAL BIOLOGY; EXONS; GENE EXPRESSION PROFILING; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN ISOFORMS; SOFTWARE;

EID: 58249098529     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-494     Document Type: Article

References (14)

1. Richard DJ Schumacher V Royer-Pokora B Roberts SGE Par4 is a coactivator for a splice isoform-specific transcriptional activation domain in WT1 Genes Dev 2001, 15(3):328-339. 312625 11159913
2. Gruber FX Hjorth-Hansen H Mikkola I Stenke L Johansen T A novel Bcr-Abl splice isoform is associated with the L248V mutation in CML patients with acquired resistance to imatinib Leukemia 2006, 20:2057-2060. 17008892
3. IGB http://www.affymetrix.com/support/developer/tools/affytools.affx
4. ExACT http://www.affymetrix.com/products/software/specific/exact.affx
5. Affymetrix Expression Console http://www.affymetrix.com/products/ software/specific/expression_console_software.affx
6. Gentleman RC Carey VJ Bates DM Bolstad B Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J Hornik K Hothorn T Huber W Iacus S Irizarry R Leisch F Li C Maechler M Rossini AJ Sawitzki G Smith C Smyth G Tierney L Yang JY Zhang J Bioconductor: Open software development for computational biology and bioinformatics Genome Biol 2004, 5(10):R80. 545600 15461798
7. Okoniewski MJ Yates T Dibben S Miller CJ An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data Genome Biol 2007, 8(5):R79. 1929135 17498294
8. Yoshida R Numata K Imoto S Nagasaki M Doi A Ueno K Miyano S Computational genome-wide discovery of aberrant splice variations with exon expression profiles Proc IEEE 7th International Symposium on Bioinformatics & Bioengineering 2007, 715-722.
9. Yoshida R Numata K Imoto S Nagasaki M Doi A Ueno K Miyano S A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST Arrays Genome Informatics 2006, 17(1):88-99. 17503359
10. Gardina PJ Clark TA Shimada B Staples MK Yang Q Veitch J Schweitzer A Awad T Sugnet C Dee S Davies C Williams A Turpaz Y Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array BMC Genomics 2006, 7:325. 1769375 17192196
11. Affymetrix Alternative transcript analysis methods for exon arrays Affymetrix Whitepaper 2005.
12. Cell File Conversion Tool http://www.affymetrix.com/Auth/support/ developer/downloads/Tools/CelFileConversion.ZIP
13. Schuler GD Epstein JA Ohkawa H Kans JA Entrez: Molecular biology database and retrieval system Methods Enzymol 1996, 266:141-162. 8743683
14. Liu G Loraine AE Shigeta R Cline M Cheng J Valmeekam V Sun S Kulp D Siani-Rose MA NetAffx: Affymetrix probesets and annotations Nucleic Acids Res 2003, 31(1):82-86. 165568 12519953