Splicy: A web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data

BMC Bioinformatics

Volumn 8, Issue SUPPL. 1, 2007, Pages

  Rambaldi, Davide ^a   Felice, Barbara ^a   Praz, Viviane ^b   Bucher, Philip ^b   Cittaro, Davide ^a   Guffanti, Alessandro ^a,c  

^a FIRC INSTITUTE OF MOLECULAR ONCOLOGY   (Italy)

^b SWISS INST FOR EXP CANCER RESEARCH   (Switzerland)

^c INSTITUTE OF BIOMEDICAL TECHNOLOGIES   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE SPLICING; GENE EXPRESSION LEVELS; GENE EXPRESSION PROFILES; GENE EXPRESSION STUDIES; MICROARRAY EXPERIMENTS; PHYSICAL STRUCTURES; REFERENCE DATABASE; WEB-BASED SOFTWARES;

BIOINFORMATICS; CELL DEATH; DISEASES; GENE EXPRESSION; MAMMALS; MAPPING; RESEARCH;

PROBES;

COMPLEMENTARY DNA;

ARTICLE; BREAST CANCER; CHROMOSOME ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; EXON; GENE FUNCTION; GENE MAPPING; GENE STRUCTURE; GENE TARGETING; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENOMICS; HUMAN; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; WEB BROWSER; ALTERNATIVE RNA SPLICING; CHROMOSOME MAP; DNA MICROARRAY; DNA PROBE; DNA SEQUENCE; EVALUATION; GENETICS; INSTRUMENTATION; INTERNET; METHODOLOGY; RNA SPLICING;

ALTERNATIVE SPLICING; CHROMOSOME MAPPING; DATABASES, GENETIC; DNA PROBES; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA SPLICE SITES; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 34248140047     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S1-S17     Document Type: Article

References (20)

1. Splicy http://bio.ifom-ieo-campus.it/splicy/
2. Venables JP Aberrant and alternative splicing in cancer Cancer Res 2004, 64(21):7647-7654. 10.1158/0008-5472.CAN-04-1910 15520162
3. Schwerk C Schulze-Osthoff K Regulation of apoptosis by alternative pre-mRNA splicing Mol Cell 2005, 19(1):1-13. 10.1016/ j.molcel.2005.05.026 15989960
4. Cartegni L Chew SL Krainer AR Listening to silence and understanding nonsense: Exonic mutations that affect splicing Nat Rev Genet 2002, 3(4):285-298. 10.1038/nrg775 11967553
5. 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(5653):2141-2144. 10.1126/science.1090100 14684825
6. Relogio A Schwager C Richter A Ansorge W Valcarcel J Optimization of oligonucleotide-based DNA microarrays Nucleic Acids Res 2002, 30(11):e51. 117213 12034852 10.1093/nar/30.11.e51
7. Affymetrix http://www.affymetrix.com
8. Lee C Roy M Analysis of alternative splicing with microarrays: Successes and challenges Genome Biol 2004, 5(7):231. 463277 15239822 10.1186/ gb-2004-5-7-231
9. Dudoit S Gentleman RC Quackenbush J Open source software for the analysis of microarray data Biotechniques 2003(Suppl):45-51. 12664684
10. Bioconductor http://www.bioconductor.org/
11. 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 10.1093/nar/gkg121
12. Tagger http://tagger.sourceforge.net/
13. Karolchik D Hinrichs AS Furey TS Roskin KM Sugnet CW Haussler D Kent WJ The UCSC Table Browser data retrieval tool Nucleic Acids Res 2004, 32: Database D493-496. 308837 14681465 10.1093/nar/gkh103
14. Praz V Jagannathan V Bucher P CleanEx: A database of heterogeneous gene expression data based on a consistent gene nomenclature Nucleic Acids Res 2004, 32: Database D542-547. 308841 14681477 10.1093/nar/gkh107
15. MySQL http://www.mysql.com
16. GD Graphic Library http://www.boutell.com/gd/
17. Stajich JE Block D Boulez K Brenner SE Chervitz SA Dagdigian C Fuellen G Gilbert JG Korf I Lapp H The Bioperl toolkit: Perl modules for the life sciences Genome Res 2002, 12(10):1611-1618. 187536 12368254 10.1101/ gr.361602
18. Overlib http://www.bosrup.com/web/overlib/
19. Maglott D Ostell J Pruitt KD Tatusova T Entrez Gene: Gene-centered information at NCBI Nucleic Acids Res 2005, 33: Database D54-58. 539985 15608257 10.1093/nar/gki031
20. Karolchik D Baertsch R Diekhans M Furey TS Hinrichs A Lu YT Roskin KM Schwartz M Sugnet CW Thomas DJ The UCSC Genome Browser Database Nucleic Acids Res 2003, 31(1):51-54. 165576 12519945 10.1093/nar/gkg129