Investigation of Splicing Quantitative Trait Loci in
The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs a...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2016-12-01
|
| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gni-14-211.pdf |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832569510946668544 |
|---|---|
| author | Wonseok Yoo Sungkyu Kyung Seonggyun Han Sangsoo Kim |
| author_facet | Wonseok Yoo Sungkyu Kyung Seonggyun Han Sangsoo Kim |
| author_sort | Wonseok Yoo |
| collection | DOAJ |
| description | The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs). In summary, this sQTL analysis provides new insight into genetic elements affecting alternative splicing patterns in Arabidopsis thaliana and the mechanism of previously reported trait-associated SNPs. |
| format | Article |
| id | doaj-art-2c11629329c14f689e36a1bf1cda8cef |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2016-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-2c11629329c14f689e36a1bf1cda8cef2025-02-02T20:58:15ZengBioMed CentralGenomics & Informatics1598-866X2234-07422016-12-0114421121510.5808/GI.2016.14.4.211182Investigation of Splicing Quantitative Trait Loci inWonseok Yoo0Sungkyu Kyung1Seonggyun Han2Sangsoo Kim3Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea.Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea.Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea.Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea.The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs). In summary, this sQTL analysis provides new insight into genetic elements affecting alternative splicing patterns in Arabidopsis thaliana and the mechanism of previously reported trait-associated SNPs.http://genominfo.org/upload/pdf/gni-14-211.pdfQTL mappingRNA-seqsQTLs |
| spellingShingle | Wonseok Yoo Sungkyu Kyung Seonggyun Han Sangsoo Kim Investigation of Splicing Quantitative Trait Loci in Genomics & Informatics QTL mapping RNA-seq sQTLs |
| title | Investigation of Splicing Quantitative Trait Loci in |
| title_full | Investigation of Splicing Quantitative Trait Loci in |
| title_fullStr | Investigation of Splicing Quantitative Trait Loci in |
| title_full_unstemmed | Investigation of Splicing Quantitative Trait Loci in |
| title_short | Investigation of Splicing Quantitative Trait Loci in |
| title_sort | investigation of splicing quantitative trait loci in |
| topic | QTL mapping RNA-seq sQTLs |
| url | http://genominfo.org/upload/pdf/gni-14-211.pdf |
| work_keys_str_mv | AT wonseokyoo investigationofsplicingquantitativetraitlociin AT sungkyukyung investigationofsplicingquantitativetraitlociin AT seonggyunhan investigationofsplicingquantitativetraitlociin AT sangsookim investigationofsplicingquantitativetraitlociin |