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The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome
Jeremy Leipzig1, Pavel Pevzner, Steffen Heber
1Department of Computer Science, College of Engineering, North Carolina State University, Raleigh, NC 27695-7566, USA.
Nucleic Acids Research
|August 5, 2004
Summary
Alternative splicing, which generates diverse transcripts, is crucial for health and disease. This study introduces a novel splicing graph approach to systematically analyze gene transcript variants, revealing extensive alternative splicing across human genes.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Alternative splicing significantly expands transcriptome diversity, impacting physiological processes, development, and disease etiology.
- Traditional case-by-case analysis of alternative splicing is inefficient and prone to errors, especially for genes with numerous splice variants.
Purpose of the Study:
- To develop a systematic approach for analyzing alternative splicing and exploring the full spectrum of transcript variants.
- To create a comprehensive database of splicing graphs for human genes.
Main Methods:
- Integration of all gene transcripts into a single splicing graph representation, where each transcript is a path and alternative splicing is shown by bifurcations.
- Compilation of transcript data from major sources including Ensembl, RefSeq, STACK, TIGR, and UniGene.
- Development of a web interface for visualizing splicing graphs, assembling transcripts, and accessing genomic sequence data.
Main Results:
- Construction of a database containing splicing graphs for human genes.
- Identification of over 1.2 million putative transcripts.
- Evidence of alternative splicing in approximately 65% of investigated genes.
- Discovery that 5% of genes may produce over 100 distinct transcripts.
Conclusions:
- The splicing graph approach provides a systematic and comprehensive method for studying alternative splicing.
- The findings highlight the extensive prevalence and complexity of alternative splicing in the human transcriptome.
- This resource facilitates deeper investigation into the functional implications of alternative splicing in biology and disease.