Model-based prediction of cis-acting RNA elements regulating tissue-specifc alternative splicing

Xin Wang, Kejun Wang, Guohua Wang, Jeremy R. Sanford, Yunlong Liu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Here we describe a model-based approach to predict cis-acting RNA elements which regulate tissue-specific alternative splicing. The model facilitates the identification of cis-acting elements (or CAE) and the estimation of their activities, considering the splicing variants between two different tissues as the combinatorial functions of multiple elements. We implement this model on a set of differentially expressed exons, between heart and liver, derived from Affymetrix GeneChip® Human Exon 1.0 ST Array sample data. Focusing on hexamers, we select top 15 motifs with greatest cumulative exon inclusion (EIC) scores as the potential as-acting elements. Eight of the total 15 hexamers are validated based on known exonic splicing regulators (ESRs) and predicted ESRs (PESRs). Permutation test demonstrates that the predicted EIC scores are statistically significant. Based on the prediction, we propose that PTB, hnRNP-B, SRp40, as well as other unknown factors are involved in the tissue-specific alternative splicing between heart and liver.

Original languageEnglish (US)
Title of host publication8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008
DOIs
StatePublished - Dec 1 2008
Event8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008 - Athens, Greece
Duration: Oct 8 2008Oct 10 2008

Publication series

Name8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

Other

Other8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008
CountryGreece
CityAthens
Period10/8/0810/10/08

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering

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    Wang, X., Wang, K., Wang, G., Sanford, J. R., & Liu, Y. (2008). Model-based prediction of cis-acting RNA elements regulating tissue-specifc alternative splicing. In 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008 [4696675] (8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008). https://doi.org/10.1109/BIBE.2008.4696675