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

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

doi:10.1109/BIBE.2008.4696675

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: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

2 Citations (Scopus)

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 language	English
Title of host publication	8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008
DOIs	https://doi.org/10.1109/BIBE.2008.4696675
Publication status	Published - 2008
Externally published	Yes
Event	8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008 - Athens, Greece Duration: 8 Oct 2008 → 10 Oct 2008

Publication series

Name	8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

Conference

Conference	8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008
Place	Greece
City	Athens
Period	8/10/08 → 10/10/08

Bibliographical note

Publication details (e.g. title, author(s), publication statuses and dates) are captured on an “AS IS” and “AS AVAILABLE” basis at the time of record harvesting from the data source. Suggestions for further amendments or supplementary information can be sent to [email protected].

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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 Article 4696675 (8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008). https://doi.org/10.1109/BIBE.2008.4696675

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title = "Model-based prediction of cis-acting RNA elements regulating tissue-specifc alternative splicing",

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{\textregistered} 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.",

author = "Xin Wang and Kejun Wang and Guohua Wang and Sanford, {Jeremy R.} and Yunlong Liu",

note = "Publication details (e.g. title, author(s), publication statuses and dates) are captured on an “AS IS” and “AS AVAILABLE” basis at the time of record harvesting from the data source. Suggestions for further amendments or supplementary information can be sent to [email protected].; 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008 ; Conference date: 08-10-2008 Through 10-10-2008",

year = "2008",

doi = "10.1109/BIBE.2008.4696675",

language = "English",

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Wang, X, Wang, K, Wang, G, Sanford, JR & 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, 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008, Athens, Greece, 8/10/08. https://doi.org/10.1109/BIBE.2008.4696675

Model-based prediction of cis-acting RNA elements regulating tissue-specifc alternative splicing. / Wang, Xin; Wang, Kejun; Wang, Guohua et al.
8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008. 2008. 4696675 (8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008).

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

TY - GEN

T1 - Model-based prediction of cis-acting RNA elements regulating tissue-specifc alternative splicing

AU - Wang, Xin

AU - Wang, Kejun

AU - Wang, Guohua

AU - Sanford, Jeremy R.

AU - Liu, Yunlong

N1 - Publication details (e.g. title, author(s), publication statuses and dates) are captured on an “AS IS” and “AS AVAILABLE” basis at the time of record harvesting from the data source. Suggestions for further amendments or supplementary information can be sent to [email protected].

PY - 2008

Y1 - 2008

N2 - 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.

AB - 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.

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DO - 10.1109/BIBE.2008.4696675

M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 9781424428458

T3 - 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

BT - 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

T2 - 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

Y2 - 8 October 2008 through 10 October 2008

ER -

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

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