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Article: PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs
Title | PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs |
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Authors | |
Issue Date | 2015 |
Publisher | Nature Publishing Group: Open Access Journals. The Journal's web site is located at http://www.nature.com/srep/index.html |
Citation | Scientific Reports, 2015, v. 5, article no. 17302 How to Cite? |
Abstract | Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets. |
Persistent Identifier | http://hdl.handle.net/10722/234399 |
ISSN | 2023 Impact Factor: 3.8 2023 SCImago Journal Rankings: 0.900 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Cheng, Z | - |
dc.contributor.author | Chu, H | - |
dc.contributor.author | Fan, Y | - |
dc.contributor.author | Li, C | - |
dc.contributor.author | Song, Y | - |
dc.contributor.author | Zhou, J | - |
dc.contributor.author | Yuen, KY | - |
dc.date.accessioned | 2016-10-14T13:46:36Z | - |
dc.date.available | 2016-10-14T13:46:36Z | - |
dc.date.issued | 2015 | - |
dc.identifier.citation | Scientific Reports, 2015, v. 5, article no. 17302 | - |
dc.identifier.issn | 2045-2322 | - |
dc.identifier.uri | http://hdl.handle.net/10722/234399 | - |
dc.description.abstract | Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets. | - |
dc.language | eng | - |
dc.publisher | Nature Publishing Group: Open Access Journals. The Journal's web site is located at http://www.nature.com/srep/index.html | - |
dc.relation.ispartof | Scientific Reports | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.title | PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs | - |
dc.type | Article | - |
dc.identifier.email | Chu, H: hinchu@hku.hk | - |
dc.identifier.email | Fan, Y: felixfan@hku.hk | - |
dc.identifier.email | Li, C: licun@hku.hk | - |
dc.identifier.email | Song, Y: songy@hku.hk | - |
dc.identifier.email | Zhou, J: jiezhou@hku.hk | - |
dc.identifier.email | Yuen, KY: kyyuen@hkucc.hku.hk | - |
dc.identifier.authority | Chu, H=rp02125 | - |
dc.identifier.authority | Song, Y=rp00488 | - |
dc.identifier.authority | Zhou, J=rp01412 | - |
dc.identifier.authority | Yuen, KY=rp00366 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1038/srep17302 | - |
dc.identifier.pmid | 26612672 | - |
dc.identifier.pmcid | PMC4661514 | - |
dc.identifier.scopus | eid_2-s2.0-84948469205 | - |
dc.identifier.hkuros | 269080 | - |
dc.identifier.volume | 5 | - |
dc.identifier.spage | article no. 17302 | - |
dc.identifier.epage | article no. 17302 | - |
dc.identifier.isi | WOS:000365396600001 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 2045-2322 | - |