Predicting Alternative Splicing Using GeneChip Data
Author Information
Author(s): Fan Wenhong, Khalid Najma, Hallahan Andrew R, Olson James M, Zhao Lue Ping
Primary Institution: Fred Hutchinson Cancer Research Center
Hypothesis
Can we develop a method to predict alternative splicing from GeneChip expression array data?
Conclusion
The two-step approach described in this paper is capable of predicting some alternative splicing from GeneChip data.
Supporting Evidence
- The method predicted 577 alternatively spliced genes when comparing normal cerebellum samples to medulloblastomas.
- Thirteen alternatively spliced genes were predicted when comparing non-metastatic medulloblastomas to metastatic ones.
- The method uses extensive repositories of GeneChip data to generate hypotheses for further validation.
Takeaway
The researchers created a method to find different versions of genes that can be made from the same DNA, using special data from GeneChip technology.
Methodology
A two-step approach was used to cluster probes into pseudo-exons and assess statistical significance of differences in probe intensity between two groups.
Potential Biases
Non-specific hybridization in expression arrays could lead to false positives and negatives.
Limitations
The method can only detect splice variants at the 3' end and does not differentiate between alternative splicing and alternative polyadenylation.
Participant Demographics
The study included 69 medulloblastoma samples (27 metastatic and 42 non-metastatic) and 4 normal cerebellum samples.
Statistical Information
P-Value
0.05
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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