Discovery the relationship between single nucleotide polymorphisms and alternative splicing events

Fang Rong Hsu; Hsien Chun Lin; Hwan You Chang

doi:10.1007/978-3-540-68017-8_132

Discovery the relationship between single nucleotide polymorphisms and alternative splicing events

Fang Rong Hsu^*, Hsien Chun Lin, Hwan You Chang

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

Abstract

Recent genome-wide analysis of alternative splicing indicate that 40–60% of human genes have alternative splice forms, suggesting that alternative splicing is one of the most significant components of the functional complexity of the human genome. Avatar (A value added transcriptome database) identified 174,546 alternative splicing events coverage of Homo sapiens through an analysis of large scale ESTs. And Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation. The refSNP (reference SNP) of dbSNP contained a total of 9,098,790 refSNPs information. The large volume of data produced by highthroughput sequencing projects is a rich and large source of SNPs and alternative splicing. The study of alternative splicing has long been a valuable subfield of molecular biology, can promote the proceeding of molecular biologic studies. We analyze more than 100,000 alternative splicing events from Avatar, producing 15,228 candidate SNPs that probable have relation between SNP and alternative splicing. We use Fisher’s exact test to confirm the result and find 1,122 significant SNPs. Further we analyze the sequence in the area that near the alternative splicing event related SNP. We find some consensus sequences in the area, which may related to alternative splicing events.

Original language	English
Title of host publication	3rd Kuala Lumpur International Conference on Biomedical Engineering 2006
Editors	Fatimah Ibrahim, Noor Azuan Abu Osman, Juliana Usman, Nahrizul Adib Kadri
Publisher	Springer Verlag
Pages	524-527
Number of pages	4
ISBN (Electronic)	9783540680161
DOIs	https://doi.org/10.1007/978-3-540-68017-8_132
State	Published - 2007
Externally published	Yes
Event	3rd Kuala Lumpur International Conference on Biomedical Engineering, Biomed 2006 - Kuala Lumpur, Malaysia Duration: 11 12 2006 → 14 12 2006

Publication series

Name	IFMBE Proceedings
Volume	15
ISSN (Print)	1680-0737
ISSN (Electronic)	1433-9277

Conference

Conference	3rd Kuala Lumpur International Conference on Biomedical Engineering, Biomed 2006
Country/Territory	Malaysia
City	Kuala Lumpur
Period	11/12/06 → 14/12/06

Bibliographical note

Publisher Copyright:
© Springer-Verlag Berlin Heidelberg 2007.

Keywords

Alternative Splicing
Bioinformatics
Single nucleotide polymorphisms

Access to Document

10.1007/978-3-540-68017-8_132

Cite this

Hsu, F. R., Lin, H. C., & Chang, H. Y. (2007). Discovery the relationship between single nucleotide polymorphisms and alternative splicing events. In F. Ibrahim, N. A. Abu Osman, J. Usman, & N. A. Kadri (Eds.), 3rd Kuala Lumpur International Conference on Biomedical Engineering 2006 (pp. 524-527). (IFMBE Proceedings; Vol. 15). Springer Verlag. https://doi.org/10.1007/978-3-540-68017-8_132

Hsu, Fang Rong ; Lin, Hsien Chun ; Chang, Hwan You. / Discovery the relationship between single nucleotide polymorphisms and alternative splicing events. 3rd Kuala Lumpur International Conference on Biomedical Engineering 2006. editor / Fatimah Ibrahim ; Noor Azuan Abu Osman ; Juliana Usman ; Nahrizul Adib Kadri. Springer Verlag, 2007. pp. 524-527 (IFMBE Proceedings).

@inproceedings{da53b20e4a274d7ea7291ceb10cab0c6,

title = "Discovery the relationship between single nucleotide polymorphisms and alternative splicing events",

abstract = "Recent genome-wide analysis of alternative splicing indicate that 40–60% of human genes have alternative splice forms, suggesting that alternative splicing is one of the most significant components of the functional complexity of the human genome. Avatar (A value added transcriptome database) identified 174,546 alternative splicing events coverage of Homo sapiens through an analysis of large scale ESTs. And Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation. The refSNP (reference SNP) of dbSNP contained a total of 9,098,790 refSNPs information. The large volume of data produced by highthroughput sequencing projects is a rich and large source of SNPs and alternative splicing. The study of alternative splicing has long been a valuable subfield of molecular biology, can promote the proceeding of molecular biologic studies. We analyze more than 100,000 alternative splicing events from Avatar, producing 15,228 candidate SNPs that probable have relation between SNP and alternative splicing. We use Fisher{\textquoteright}s exact test to confirm the result and find 1,122 significant SNPs. Further we analyze the sequence in the area that near the alternative splicing event related SNP. We find some consensus sequences in the area, which may related to alternative splicing events.",

keywords = "Alternative Splicing, Bioinformatics, Single nucleotide polymorphisms",

author = "Hsu, {Fang Rong} and Lin, {Hsien Chun} and Chang, {Hwan You}",

note = "Publisher Copyright: {\textcopyright} Springer-Verlag Berlin Heidelberg 2007.; 3rd Kuala Lumpur International Conference on Biomedical Engineering, Biomed 2006 ; Conference date: 11-12-2006 Through 14-12-2006",

year = "2007",

doi = "10.1007/978-3-540-68017-8_132",

language = "英语",

series = "IFMBE Proceedings",

publisher = "Springer Verlag",

pages = "524--527",

editor = "Fatimah Ibrahim and {Abu Osman}, {Noor Azuan} and Juliana Usman and Kadri, {Nahrizul Adib}",

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Hsu, FR, Lin, HC & Chang, HY 2007, Discovery the relationship between single nucleotide polymorphisms and alternative splicing events. in F Ibrahim, NA Abu Osman, J Usman & NA Kadri (eds), 3rd Kuala Lumpur International Conference on Biomedical Engineering 2006. IFMBE Proceedings, vol. 15, Springer Verlag, pp. 524-527, 3rd Kuala Lumpur International Conference on Biomedical Engineering, Biomed 2006, Kuala Lumpur, Malaysia, 11/12/06. https://doi.org/10.1007/978-3-540-68017-8_132

Discovery the relationship between single nucleotide polymorphisms and alternative splicing events. / Hsu, Fang Rong; Lin, Hsien Chun; Chang, Hwan You.
3rd Kuala Lumpur International Conference on Biomedical Engineering 2006. ed. / Fatimah Ibrahim; Noor Azuan Abu Osman; Juliana Usman; Nahrizul Adib Kadri. Springer Verlag, 2007. p. 524-527 (IFMBE Proceedings; Vol. 15).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Discovery the relationship between single nucleotide polymorphisms and alternative splicing events

AU - Hsu, Fang Rong

AU - Lin, Hsien Chun

AU - Chang, Hwan You

N1 - Publisher Copyright: © Springer-Verlag Berlin Heidelberg 2007.

PY - 2007

Y1 - 2007

N2 - Recent genome-wide analysis of alternative splicing indicate that 40–60% of human genes have alternative splice forms, suggesting that alternative splicing is one of the most significant components of the functional complexity of the human genome. Avatar (A value added transcriptome database) identified 174,546 alternative splicing events coverage of Homo sapiens through an analysis of large scale ESTs. And Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation. The refSNP (reference SNP) of dbSNP contained a total of 9,098,790 refSNPs information. The large volume of data produced by highthroughput sequencing projects is a rich and large source of SNPs and alternative splicing. The study of alternative splicing has long been a valuable subfield of molecular biology, can promote the proceeding of molecular biologic studies. We analyze more than 100,000 alternative splicing events from Avatar, producing 15,228 candidate SNPs that probable have relation between SNP and alternative splicing. We use Fisher’s exact test to confirm the result and find 1,122 significant SNPs. Further we analyze the sequence in the area that near the alternative splicing event related SNP. We find some consensus sequences in the area, which may related to alternative splicing events.

AB - Recent genome-wide analysis of alternative splicing indicate that 40–60% of human genes have alternative splice forms, suggesting that alternative splicing is one of the most significant components of the functional complexity of the human genome. Avatar (A value added transcriptome database) identified 174,546 alternative splicing events coverage of Homo sapiens through an analysis of large scale ESTs. And Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation. The refSNP (reference SNP) of dbSNP contained a total of 9,098,790 refSNPs information. The large volume of data produced by highthroughput sequencing projects is a rich and large source of SNPs and alternative splicing. The study of alternative splicing has long been a valuable subfield of molecular biology, can promote the proceeding of molecular biologic studies. We analyze more than 100,000 alternative splicing events from Avatar, producing 15,228 candidate SNPs that probable have relation between SNP and alternative splicing. We use Fisher’s exact test to confirm the result and find 1,122 significant SNPs. Further we analyze the sequence in the area that near the alternative splicing event related SNP. We find some consensus sequences in the area, which may related to alternative splicing events.

KW - Alternative Splicing

KW - Bioinformatics

KW - Single nucleotide polymorphisms

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AN - SCOPUS:84928891981

T3 - IFMBE Proceedings

SP - 524

EP - 527

BT - 3rd Kuala Lumpur International Conference on Biomedical Engineering 2006

A2 - Ibrahim, Fatimah

A2 - Abu Osman, Noor Azuan

A2 - Usman, Juliana

A2 - Kadri, Nahrizul Adib

PB - Springer Verlag

T2 - 3rd Kuala Lumpur International Conference on Biomedical Engineering, Biomed 2006

Y2 - 11 December 2006 through 14 December 2006

ER -

Discovery the relationship between single nucleotide polymorphisms and alternative splicing events

Abstract

Publication series

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Bibliographical note

Keywords

Access to Document

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