Venables JP: Unbalanced alternative splicing and its significance in cancer. Bioessays. 2006, 28: 378-386. 10.1002/bies.20390.
Article
PubMed
CAS
Google Scholar
Faustino NA, Cooper TA: Pre-mRNA splicing and human disease. Genes Dev. 2003, 17: 419-437. 10.1101/gad.1048803.
Article
PubMed
CAS
Google Scholar
Bracco L, Kearsey J: The relevance of alternative RNA splicing to pharmacogenomics. Trends Biotechnol. 2003, 21: 346-353. 10.1016/S0167-7799(03)00146-X.
Article
PubMed
CAS
Google Scholar
Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD: Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science. 2003, 302: 2141-2144. 10.1126/science.1090100.
Article
PubMed
CAS
Google Scholar
Modrek B, Lee C: A genomic view of alternative splicing. Nat Genet. 2002, 30: 13-19. 10.1038/ng0102-13.
Article
PubMed
CAS
Google Scholar
Okoniewski MJ, Hey Y, Pepper SD, Miller C: High correspondence between Affymetrix exon and standard expression arrays. Biotechniques. 2007, 42: 181-185.
Article
PubMed
CAS
Google Scholar
Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, et al: Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 2005, 33: e175-10.1093/nar/gni179.
Article
PubMed
PubMed Central
Google Scholar
Michalak P: RNA world - the dark matter of evolutionary genomics. J Evol Biol. 2006, 19: 1768-1774. 10.1111/j.1420-9101.2006.01141.x.
Article
PubMed
CAS
Google Scholar
Johnson JM, Edwards S, Shoemaker D, Schadt EE: Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 2005, 21: 93-102. 10.1016/j.tig.2004.12.009.
Article
PubMed
CAS
Google Scholar
Dennis C: The brave new world of RNA. Nature. 2002, 418: 122-124. 10.1038/418122a.
Article
PubMed
CAS
Google Scholar
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics. 2001, 29: 365-371. 10.1038/ng1201-365.
Article
PubMed
CAS
Google Scholar
Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z: Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics. 2005, 6: 107-10.1186/1471-2105-6-107.
Article
PubMed
PubMed Central
Google Scholar
Hwang KB, Kong SW, Greenberg SA, Park PJ: Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics. 2004, 5: 159-10.1186/1471-2105-5-159.
Article
PubMed
PubMed Central
Google Scholar
Leong HS, Yates T, Wilson C, Miller CJ: ADAPT: A Database of Affymetrix Probesets and Transcripts. Bioinformatics. 2005, 21: 2552-2553. 10.1093/bioinformatics/bti359.
Article
PubMed
CAS
Google Scholar
Miller C, Gurd J, Brass A: A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases. Bioinformatics. 1999, 15: 111-121. 10.1093/bioinformatics/15.2.111.
Article
PubMed
CAS
Google Scholar
Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, et al: An overview of Ensembl. Genome Res. 2004, 14: 925-928. 10.1101/gr.1860604.
Article
PubMed
CAS
PubMed Central
Google Scholar
Google Maps API. [http://www.google.com/apis/maps/]
X:MAP. [http://xmap.picr.man.ac.uk]
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5: R80-10.1186/gb-2004-5-10-r80.
Article
PubMed
PubMed Central
Google Scholar
Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E: EnsMart: a generic system for fast and flexible access to biological data. Genome Res. 2004, 14: 160-169. 10.1101/gr.1645104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W: BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics. 2005, 21: 3439-3440. 10.1093/bioinformatics/bti525.
Article
PubMed
CAS
Google Scholar
Seifert M, Scherf M, Epple A, Werner T: Multievidence microarray mining. Trends Genet. 2005, 21: 553-558. 10.1016/j.tig.2005.07.011.
Article
PubMed
CAS
Google Scholar
Paterson Institute for Cancer Research Bioinformatics Group Homepage. [http://bioinformatics.picr.man.ac.uk]
Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 2001, 98: 5116-5121. 10.1073/pnas.091062498.
Article
PubMed
CAS
PubMed Central
Google Scholar
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31: e15-10.1093/nar/gng015.
Article
PubMed
PubMed Central
Google Scholar
Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003, 4: 249-264. 10.1093/biostatistics/4.2.249.
Article
PubMed
Google Scholar
Affymetrix: Alternative Transcript Analysis Methods for Exon Arrays v.1.1. 2005, Santa Clara: Affymetrix
Google Scholar
Clark TA, Sugnet CW, Ares M: Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science. 2002, 296: 907-910. 10.1126/science.1069415.
Article
PubMed
CAS
Google Scholar
Cline MS, Blume J, Cawley S, Clark TA, Hu JS, Lu G, Salomonis N, Wang H, Williams A: ANOSVA: a statistical method for detecting splice variation from expression data. Bioinformatics. 2005, 21 (Suppl 1): i107-115. 10.1093/bioinformatics/bti1010.
Article
PubMed
CAS
Google Scholar
La Rosa P, Viara E, Hupe P, Pierron G, Liva S, Neuvial P, Brito I, Lair S, Servant N, Robine N, et al: VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinformatics. 2006, 22: 2066-2073. 10.1093/bioinformatics/btl359.
Article
PubMed
CAS
Google Scholar
Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, et al: The ENCODE Project at UC Santa Cruz. Nucleic Acids Res. 2007, 35 (Database issue): D663-D667. 10.1093/nar/gkl1017.
Article
PubMed
CAS
PubMed Central
Google Scholar
Viswanath L, Lu Y, Fox G: Genome display tool: visualizing features in complex data sets. Source Code Biol Med. 2007, 2: 1-10.1186/1751-0473-2-1.
Article
PubMed
PubMed Central
Google Scholar
Dolan M, Holden CC, Beard MK, Bult CJ: EGenomes as geography: using GIS technology to build interactive genome feature maps. BMC Bioinformatics. 2006, 7: 416-10.1186/1471-2105-7-416.
Article
PubMed
PubMed Central
Google Scholar
Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, et al: The UCSC genome browser database: update 2007. Nucleic Acids Res. 2007, 35 (Database issue): D668-D673. 10.1093/nar/gkl928.
Article
PubMed
CAS
PubMed Central
Google Scholar
Netaffx Analysis Center. [http://www.affymetrix.com/analysis/index.affx]
exonmap. [http://www.bioconductor.org/packages/2.0/bioc/html/exonmap.html]
Guigo R, Flicek P, Abril J, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic V, Birney E, et al: EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 2006, 7 (Suppl 1): S2-10.1186/gb-2006-7-s1-s2.
Article
PubMed
PubMed Central
Google Scholar