Abstract
BackgroundThe Affymetrix™ technology is nowadays a well-established method for the analysis of gene expression profiles in cancer research studies. However, changes in gene expression levels are not the only way to link genes and disease. The existence of gene isoforms specifically linked with cancer or apoptosis is increasingly found in literature. Hence it is of great interest to associate the results of a gene expression study with updated evidences on the transcript structure and its possible variants.ResultsWe present here a web-based software tool, Splicy, whose primary task is to retrieve data on the mapping of Affymetrix™ probes to single exons of gene transcripts and displaying graphically this information projected on the gene physical structure.Starting from a list of Affymetrix™ probesets the program produces a series of graphical displays, each relative to a transcript associated with the gene targeted by a given probe. The information on the transcript-by-transcript and exon-by-exon mapping of probe pairs can be retrieved both graphically and in the form of tab-separated files. The mapping of single probes to NCBI RefSeq or EMBL cDNAs is handled by the ISREC mapping tables used in the CleanEx Expression Reference Database Project. We currently maintain these mappings for most popular human and mouse Affymetrix™ chips, and Splicy can be queried for matches with human and mouse NCBI RefSeq or EMBL cDNAs.ConclusionSplicy generates probeset annotations and images describing the relation between the single probes and intron/exon structure of the target transcript in all its known variants. We think that Splicy will be useful for giving to the researcher a clearer picture of the possible transcript variants linked with a given gene and an additional view on the interpretation of microarray experiment data. Splicy is publicly available and has been realized in the framework of a bioinformatics grant from the Italian Cancer Research Association.
Highlights
The AffymetrixTM technology is nowadays a well-established method for the analysis of gene expression profiles in cancer research studies
It is well known that cancer is strictly associated with relevant changes in gene expression; it is crucial to know whether cancer involves sensible changes in mRNA splicing patterns and isoform expression levels
Through a Bioconductor [9,10] function, we have made some plots of single probes Perfect Matches (PM) from hybridization samples of breast cancer and normal breast tissue
Summary
The AffymetrixTM technology is nowadays a well-established method for the analysis of gene expression profiles in cancer research studies. It is of great interest to associate the results of a gene expression study with updated evidences on the transcript structure and its possible variants. Alternative splicing is a biological process that generates multiple different transcripts from the same precursor mRNA. It is an important regulatory mechanism for eukaryotic gene expression occurring in about 40–60% of human genes. It is well known that cancer is strictly associated with relevant changes in gene expression; it is crucial to know whether cancer involves sensible changes in mRNA splicing patterns and isoform expression levels. Genome wide methods are providing a better and more complete understanding of the functional relevance of splice variants and genetic mechanisms of disease. Microarrays are a widely used high-throughput technology for studying gene expression and regulation on a global scale
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
