Additional file 2: of Extensive variation between tissues in allele specific expression in an outbred mammal

Additional file 18: Table S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NZ combination. (XLSX 45...

Additional file 2: of Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

Ramya Raviram (455970)
Pedro Rocha (386032)
Vincent Luo (6080330)
Emily Swanzey (2551705)
Emily Miraldi (6080333)
Edward Chuong (6080336)
CĂŠdric Feschotte (3439277)
Richard Bonneau (4318)
Jane Skok (6080339)

December 2018

Supplementary Tables. This file contains 5 supplementary tables for this paper. Table S1. List of 4T...

Additional file 1 of Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Wencheng Zong (8025542)
Jinbu Wang (2359150)
Runze Zhao (3401315)
Naiqi Niu (17112914)
Yanfang Su (706280)
Ziping Hu (17112917)
Xin Liu (43569)
Xinhua Hou (108350)
Ligang Wang (347845)
Lixian Wang (465239)
Longchao Zhang (10736706)

October 2023

Additional file 1: Table S1. Sample information. Table S2. TE reference sequence. Table S3. Primers ...

Additional file 1: of Extensive variation between tissues in allele specific expression in an outbred mammal

Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Benjamin Hayes (1986859)
Majid Khansefid (3398150)
Leah Marett (1986853)
Catriona Millen (3398147)
Thuy Nguyen (160049)
Michael Goddard (3398153)

November 2015

Contains supplementary material including Figures S1Â - S7, as well as Tables S1, S2, S6 - S9, S11 -...

Additional file 1 of Gene-specific patterns of expression variation across organs and species

Alessandra Breschi (3448616)
Sarah Djebali (189529)
Jesse Gillis (174666)
Dmitri Pervouchine (3448622)
Alex Dobin (189598)
Carrie Davis (3448619)
Thomas Gingeras (13717)
Roderic GuigĂł (3448643)

July 2016

Figures S1âS13. File with all supplementary figures, from S1 to S13. (PDF 871 kb

Additional file 9: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 ...

Additional file 3: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S12. GWAS using SNP-chip data. The detailed results of p-values for each SNP in GWA studies fo...

Additional file 5: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S3. 2âĂâ2 tables for the overlap between exon and intron analyses. (XLSX 15 kb

Additional file 6: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S4. Genes that display significant differential splicing cross tissues. (XLSX 18699 kb

Additional file 8: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S6. Summary of significant cis splicing sQTLs (within 1Â Mb distance to the exon). (XLSX 14902...

Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S5. Genes that display significant differential splicing between breeds. (XLSX 38 kb

Additional file 3: Table S2. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

Hung-ying Lin (4519942)
Qiang Liu (166143)
Xiao Li (107004)
Jinliang Yang (588520)
Sanzhen Liu (102504)
Yinlian Huang (4519939)
Michael Scanlon (791403)
Dan Nettleton (6085)
Patrick Schnable (721002)

October 2017

Functional enrichment and GO term enrichment tests. a Functional enrichment tests of genes that exhi...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
University of Groningen
Wellcome Sanger Institute
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
Arctic Centre, Univ. of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1: of Decrease of gene expression diversity during domestication of animals and plants

Wei Liu (20030)
Lei Chen (54296)
Shilai Zhang (4633828)
Fengyi Hu (4633831)
Zheng Wang (25883)
Jun Lyu (6201101)
Bao Wang (488990)
Hui Xiang (633635)
Ruoping Zhao (234334)
Zhixi Tian (4017083)
Song Ge (48585)
Wen Wang (6570)

January 2019

Figures S1-S9 and Table S1 to Table S7 and Table S12 to Table S13. (DOCX 1736 kb

Additional file 1: of Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

K. Kemper (3511319)
M. Littlejohn (3511313)
T. Lopdell (3511301)
B. Hayes (3511316)
L. Bennett (3511307)
R. Williams (3511298)
X. Xu (771131)
P. Visscher (3511304)
M. Carrick (3511310)
M. Goddard (3486104)

November 2016

Supplementary Materials. This document contains supplementary Tables S1-S5 and supplementary Figures...

Additional file 18: Table S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NZ combination. (XLSX 45...

Additional file 2: of Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

Ramya Raviram (455970)
Pedro Rocha (386032)
Vincent Luo (6080330)
Emily Swanzey (2551705)
Emily Miraldi (6080333)
Edward Chuong (6080336)
CĂŠdric Feschotte (3439277)
Richard Bonneau (4318)
Jane Skok (6080339)

December 2018

Supplementary Tables. This file contains 5 supplementary tables for this paper. Table S1. List of 4T...

Additional file 1 of Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Wencheng Zong (8025542)
Jinbu Wang (2359150)
Runze Zhao (3401315)
Naiqi Niu (17112914)
Yanfang Su (706280)
Ziping Hu (17112917)
Xin Liu (43569)
Xinhua Hou (108350)
Ligang Wang (347845)
Lixian Wang (465239)
Longchao Zhang (10736706)

October 2023

Additional file 1: Table S1. Sample information. Table S2. TE reference sequence. Table S3. Primers ...

Additional file 1: of Extensive variation between tissues in allele specific expression in an outbred mammal

Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Benjamin Hayes (1986859)
Majid Khansefid (3398150)
Leah Marett (1986853)
Catriona Millen (3398147)
Thuy Nguyen (160049)
Michael Goddard (3398153)

November 2015

Contains supplementary material including Figures S1Â - S7, as well as Tables S1, S2, S6 - S9, S11 -...

Additional file 1 of Gene-specific patterns of expression variation across organs and species

Alessandra Breschi (3448616)
Sarah Djebali (189529)
Jesse Gillis (174666)
Dmitri Pervouchine (3448622)
Alex Dobin (189598)
Carrie Davis (3448619)
Thomas Gingeras (13717)
Roderic GuigĂł (3448643)

July 2016

Figures S1âS13. File with all supplementary figures, from S1 to S13. (PDF 871 kb

Additional file 9: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 ...

Additional file 3: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S12. GWAS using SNP-chip data. The detailed results of p-values for each SNP in GWA studies fo...

Additional file 5: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S3. 2âĂâ2 tables for the overlap between exon and intron analyses. (XLSX 15 kb

Additional file 6: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S4. Genes that display significant differential splicing cross tissues. (XLSX 18699 kb

Additional file 8: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S6. Summary of significant cis splicing sQTLs (within 1Â Mb distance to the exon). (XLSX 14902...

Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S5. Genes that display significant differential splicing between breeds. (XLSX 38 kb

Additional file 3: Table S2. of Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

Hung-ying Lin (4519942)
Qiang Liu (166143)
Xiao Li (107004)
Jinliang Yang (588520)
Sanzhen Liu (102504)
Yinlian Huang (4519939)
Michael Scanlon (791403)
Dan Nettleton (6085)
Patrick Schnable (721002)

October 2017

Functional enrichment and GO term enrichment tests. a Functional enrichment tests of genes that exhi...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
University of Groningen
Wellcome Sanger Institute
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
Arctic Centre, Univ. of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1: of Decrease of gene expression diversity during domestication of animals and plants

Wei Liu (20030)
Lei Chen (54296)
Shilai Zhang (4633828)
Fengyi Hu (4633831)
Zheng Wang (25883)
Jun Lyu (6201101)
Bao Wang (488990)
Hui Xiang (633635)
Ruoping Zhao (234334)
Zhixi Tian (4017083)
Song Ge (48585)
Wen Wang (6570)

January 2019

Figures S1-S9 and Table S1 to Table S7 and Table S12 to Table S13. (DOCX 1736 kb

Additional file 1: of Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

K. Kemper (3511319)
M. Littlejohn (3511313)
T. Lopdell (3511301)
B. Hayes (3511316)
L. Bennett (3511307)
R. Williams (3511298)
X. Xu (771131)
P. Visscher (3511304)
M. Carrick (3511310)
M. Goddard (3486104)

November 2016

Supplementary Materials. This document contains supplementary Tables S1-S5 and supplementary Figures...

Additional file 18: Table S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NZ combination. (XLSX 45...

Additional file 2: of Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

Ramya Raviram (455970)
Pedro Rocha (386032)
Vincent Luo (6080330)
Emily Swanzey (2551705)
Emily Miraldi (6080333)
Edward Chuong (6080336)
CĂŠdric Feschotte (3439277)
Richard Bonneau (4318)
Jane Skok (6080339)

December 2018

Supplementary Tables. This file contains 5 supplementary tables for this paper. Table S1. List of 4T...

Additional file 1 of Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Wencheng Zong (8025542)
Jinbu Wang (2359150)
Runze Zhao (3401315)
Naiqi Niu (17112914)
Yanfang Su (706280)
Ziping Hu (17112917)
Xin Liu (43569)
Xinhua Hou (108350)
Ligang Wang (347845)
Lixian Wang (465239)
Longchao Zhang (10736706)

October 2023

Additional file 1: Table S1. Sample information. Table S2. TE reference sequence. Table S3. Primers ...

Additional file 2: of Extensive variation between tissues in allele specific expression in an outbred mammal

Abstract

Extracted data

Additional file 2: of Extensive variation between tissues in allele specific expression in an outbred mammal

Abstract

Extracted data

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