JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts
| Publication Date: |
2018-03-06
|
|---|---|
| Publisher: |
Oxford University Press
|
| Print ISSN: |
1367-4803
|
| Electronic ISSN: |
1460-2059
|
| Topics: |
Biology
Computer Science
Medicine
|
| Published by: |
| _version_ | 1836398817056915456 |
|---|---|
| autor | Chatzinakos C, Lee D, Webb B, et al. |
| beschreibung | Motivation To increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools assume homogeneous cohorts, our G ene-level J oint A nalysis of functional SNPs in C osmopolitan C ohorts (JEPEGMIX) method accommodates cosmopolitan cohorts by using heterogeneous panels. However, JEPGMIX relies on brain eQTLs from older gene expression studies and does not adjust for background enrichment in GWAS signals. Results We propose JEPEGMIX2, an extension of JEPEGMIX. When compared to JPEGMIX, it uses (i) cis-eQTL SNPs from the latest expression studies and (ii) brains specific (sub)tissues and tissues other than brain. JEPEGMIX2 also (i) avoids accumulating averagely enriched polygenic information by adjusting for background enrichment and (ii) to avoid an increase in false positive rates for studies with numerous highly enriched (above the background) genes, it outputs gene q -values based on Holm adjustment of P -values. Availability and implementation https://github.com/Chatzinakos/JEPEGMIX2 . Contact chris.chatzinakos@vcuhealth.org Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online. |
| citation_standardnr | 6180433 |
| datenlieferant | ipn_articles |
| feed_id | 2184 |
| feed_publisher | Oxford University Press |
| feed_publisher_url | http://global.oup.com/ |
| insertion_date | 2018-03-06 |
| journaleissn | 1460-2059 |
| journalissn | 1367-4803 |
| publikationsjahr_anzeige | 2018 |
| publikationsjahr_facette | 2018 |
| publikationsjahr_intervall | 7984:2015-2019 |
| publikationsjahr_sort | 2018 |
| publisher | Oxford University Press |
| quelle | Bioinformatics |
| relation | https://academic.oup.com/bioinformatics/article/34/2/286/4158028?rss=1 |
| search_space | articles |
| shingle_author_1 | Chatzinakos C, Lee D, Webb B, et al. |
| shingle_author_2 | Chatzinakos C, Lee D, Webb B, et al. |
| shingle_author_3 | Chatzinakos C, Lee D, Webb B, et al. |
| shingle_author_4 | Chatzinakos C, Lee D, Webb B, et al. |
| shingle_catch_all_1 | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts Motivation To increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools assume homogeneous cohorts, our G ene-level J oint A nalysis of functional SNPs in C osmopolitan C ohorts (JEPEGMIX) method accommodates cosmopolitan cohorts by using heterogeneous panels. However, JEPGMIX relies on brain eQTLs from older gene expression studies and does not adjust for background enrichment in GWAS signals. Results We propose JEPEGMIX2, an extension of JEPEGMIX. When compared to JPEGMIX, it uses (i) cis-eQTL SNPs from the latest expression studies and (ii) brains specific (sub)tissues and tissues other than brain. JEPEGMIX2 also (i) avoids accumulating averagely enriched polygenic information by adjusting for background enrichment and (ii) to avoid an increase in false positive rates for studies with numerous highly enriched (above the background) genes, it outputs gene q -values based on Holm adjustment of P -values. Availability and implementation https://github.com/Chatzinakos/JEPEGMIX2 . Contact chris.chatzinakos@vcuhealth.org Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online. Chatzinakos C, Lee D, Webb B, et al. Oxford University Press 1367-4803 13674803 1460-2059 14602059 |
| shingle_catch_all_2 | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts Motivation To increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools assume homogeneous cohorts, our G ene-level J oint A nalysis of functional SNPs in C osmopolitan C ohorts (JEPEGMIX) method accommodates cosmopolitan cohorts by using heterogeneous panels. However, JEPGMIX relies on brain eQTLs from older gene expression studies and does not adjust for background enrichment in GWAS signals. Results We propose JEPEGMIX2, an extension of JEPEGMIX. When compared to JPEGMIX, it uses (i) cis-eQTL SNPs from the latest expression studies and (ii) brains specific (sub)tissues and tissues other than brain. JEPEGMIX2 also (i) avoids accumulating averagely enriched polygenic information by adjusting for background enrichment and (ii) to avoid an increase in false positive rates for studies with numerous highly enriched (above the background) genes, it outputs gene q -values based on Holm adjustment of P -values. Availability and implementation https://github.com/Chatzinakos/JEPEGMIX2 . Contact chris.chatzinakos@vcuhealth.org Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online. Chatzinakos C, Lee D, Webb B, et al. Oxford University Press 1367-4803 13674803 1460-2059 14602059 |
| shingle_catch_all_3 | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts Motivation To increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools assume homogeneous cohorts, our G ene-level J oint A nalysis of functional SNPs in C osmopolitan C ohorts (JEPEGMIX) method accommodates cosmopolitan cohorts by using heterogeneous panels. However, JEPGMIX relies on brain eQTLs from older gene expression studies and does not adjust for background enrichment in GWAS signals. Results We propose JEPEGMIX2, an extension of JEPEGMIX. When compared to JPEGMIX, it uses (i) cis-eQTL SNPs from the latest expression studies and (ii) brains specific (sub)tissues and tissues other than brain. JEPEGMIX2 also (i) avoids accumulating averagely enriched polygenic information by adjusting for background enrichment and (ii) to avoid an increase in false positive rates for studies with numerous highly enriched (above the background) genes, it outputs gene q -values based on Holm adjustment of P -values. Availability and implementation https://github.com/Chatzinakos/JEPEGMIX2 . Contact chris.chatzinakos@vcuhealth.org Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online. Chatzinakos C, Lee D, Webb B, et al. Oxford University Press 1367-4803 13674803 1460-2059 14602059 |
| shingle_catch_all_4 | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts Motivation To increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools assume homogeneous cohorts, our G ene-level J oint A nalysis of functional SNPs in C osmopolitan C ohorts (JEPEGMIX) method accommodates cosmopolitan cohorts by using heterogeneous panels. However, JEPGMIX relies on brain eQTLs from older gene expression studies and does not adjust for background enrichment in GWAS signals. Results We propose JEPEGMIX2, an extension of JEPEGMIX. When compared to JPEGMIX, it uses (i) cis-eQTL SNPs from the latest expression studies and (ii) brains specific (sub)tissues and tissues other than brain. JEPEGMIX2 also (i) avoids accumulating averagely enriched polygenic information by adjusting for background enrichment and (ii) to avoid an increase in false positive rates for studies with numerous highly enriched (above the background) genes, it outputs gene q -values based on Holm adjustment of P -values. Availability and implementation https://github.com/Chatzinakos/JEPEGMIX2 . Contact chris.chatzinakos@vcuhealth.org Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online. Chatzinakos C, Lee D, Webb B, et al. Oxford University Press 1367-4803 13674803 1460-2059 14602059 |
| shingle_title_1 | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts |
| shingle_title_2 | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts |
| shingle_title_3 | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts |
| shingle_title_4 | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts |
| timestamp | 2025-06-30T23:33:06.326Z |
| titel | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts |
| titel_suche | JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts |
| topic | W SQ-SU WW-YZ |
| uid | ipn_articles_6180433 |