Additional file 2: of Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

Additional file 2: of Evidence from genome wide association studies implicates reduced control of Epstein-Barr virus infection in multiple sclerosis susceptibility

Ali Afrasiabi (6652580)
Grant Parnell (228200)
Nicole Fewings (6652583)
Stephen Schibeci (753421)
Monica Basuki (787103)
Ramya Chandramohan (6652586)
Yuan Zhou (179597)
Bruce Taylor (4417426)
David Brown (71846)
Sanjay Swaminathan (392322)
Fiona McKay (753423)
Graeme Stewart (208243)
David Booth (228203)

April 2019

Figure S1. eQTL data of MS risk variants in whole blood (A) and LCLs (B). Figure S2. Identifying gen...

Additional file 3: Table S2. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio GarcĂa (4411630)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Results of differential expression analysis on RNA-seq data. Features are defined in the GTF file in...

Additional file 6: of T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients

Miranda Houtman (5700545)
Louise Ekholm (5567462)
Espen Hesselberg (5700548)
Karine Chemin (221751)
Vivianne Malmström (4151)
Ann Reed (5700551)
Ingrid Lundberg (3497318)
Leonid Padyukov (39206)

August 2018

Differentially expressed genes in CD4+ T cells of HLA-DRB1*03-positive and -negative myositis patien...

Additional file 3: of Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

Amanda McGovern (123689)
Stefan Schoenfelder (115930)
Paul Martin (7160)
Jonathan Massey (283320)
Kate Duffus (3353354)
Darren Plant (176475)
Annie Yarwood (3353351)
Arthur Pratt (3491927)
Amy Anderson (3491921)
John Isaacs (840151)
Julie Diboll (3491924)
Nishanthi Thalayasingam (3491918)
Caroline Ospelt (3366500)
Anne Barton (23499)
Jane Worthington (23502)
Peter Fraser (32141)
Stephen Eyre (424544)
Gisela Orozco (3353348)

November 2016

Contains the normalised expression values for CD4+ T-cells obtained from NRHV participants. (TXT 26 ...

Additional file 2: Figures S1âS14. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio GarcĂa (4411630)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Figure S1. Comparison of longer and shorter CD4+ T cell activation timecourses. Figure S2. Summary d...

Additional file 1: Table S1. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio GarcĂa (4411630)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Gene modules inferred from WGCNA analysis of microarray time-course. Expression fold changes and ass...

Additional file 2: of Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Ana Márquez (467807)
Martin Kerick (234936)
Alexandra Zhernakova (102388)
Javier Gutierrez-Achury (6109181)
Wei-Min Chen (110472)
Suna Onengut-Gumuscu (282049)
Isidoro González-Álvaro (118679)
Luis Rodriguez-Rodriguez (430986)
Raquel Rios-Fernández (6109184)
Miguel González-Gay (3587198)
Maureen Mayes (3464129)
Soumya Raychaudhuri (229153)
Stephen Rich (4035059)
Cisca Wijmenga (32954)
Javier Martín (2584444)

December 2018

Table S3. Results of the subset-based meta-analysis for the lead variants showing evidence of opposi...

Additional file 7: of Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network

Arianne Richard (3412289)
James Peters (3412283)
James Lee (212552)
Golnaz Vahedi (394496)
Alejandro SchĂ¤ffer (3412292)
Richard Siegel (3412286)
Paul Lyons (18632)
Kenneth Smith (149075)

July 2016

The best-associated SNP is listed for each cis-eQTL (FDR <Â 0.1). Studies that have previously ident...

Additional file 9: Table S7a. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio García (760108)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Autoimmune disease COGS gene prioritisation. Overall COGS gene scores (COGS_Overall_Gene_Score) for ...

Additional file 1: of The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Matzaraki, Vasiliki
Magadi Gopalaiah, Vinod Kumar
Wijmenga, Cisca
Zhernakova, Sasha
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Translational Immunology Groningen (TRIGR)

April 2017

Imputed MHC classic alleles and amino acids for infectious diseases. (XLSX 40 kb

Additional file 1: of Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Ana Márquez (467807)
Martin Kerick (234936)
Alexandra Zhernakova (102388)
Javier Gutierrez-Achury (6109181)
Wei-Min Chen (110472)
Suna Onengut-Gumuscu (282049)
Isidoro González-Álvaro (118679)
Luis Rodriguez-Rodriguez (430986)
Raquel Rios-Fernández (6109184)
Miguel González-Gay (3587198)
Maureen Mayes (3464129)
Soumya Raychaudhuri (229153)
Stephen Rich (4035059)
Cisca Wijmenga (32954)
Javier Martín (2584444)

December 2018

Table S1. Case/control datasets included in the study. Table S2. Loci reaching genome-wide level of ...

Additional file 2: Table S2. of Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease

M. Olsson (3585725)
M. Kierczak (3585737)
Å. Karlsson (3585746)
J. Jabłońska (3585731)
P. Leegwater (3585713)
M. Koltookian (3585728)
J. Abadie (3585722)
C. De Citres (3585734)
A. Thomas (2264929)
Å. Hedhammar (3585740)
L. Tintle (3585716)
K. Lindblad-Toh (3585743)
J. Meadows (3585719)

April 2016

Phenotypic overlap observed within the genetic test cohort. Table S3. Primers and Probes used in ana...

Additional file 1 of Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses

van Deuren, Rosanne C.
Arts, Peer
Cavalli, Giulio
Jaeger, Martin
Steehouwer, Marloes
van de Vorst, Maartje
Gilissen, Christian
Joosten, Leo A. B.
Dinarello, Charles A.
Mhlanga, Musa M.
Magadi Gopalaiah, Vinod Kumar
Netea, Mihai G.
van de Veerdonk, Frank L.
Hoischen, Alexander
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
University of Colorado

May 2021

Additional file 1: Supplementary Tables. Table S1. Variant grouping strategies of 48 Interleukin-1 p...

Additional file 1: of Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci

Jared Dean (3288975)
Ryan Emerson (2591968)
Marissa Vignali (482139)
Anna Sherwood (3289119)
Mark Rieder (44223)
Christopher Carlson (707407)
Harlan Robins (88134)

November 2015

Table listing the number of sequences observed in the study (including total, unique, productive, an...

Additional file 2: of T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients

Miranda Houtman (5700545)
Louise Ekholm (5567462)
Espen Hesselberg (5700548)
Karine Chemin (221751)
Vivianne Malmström (4151)
Ann Reed (5700551)
Ingrid Lundberg (3497318)
Leonid Padyukov (39206)

August 2018

Differentially expressed genes for CD4+ T cells of PM and DM patients. Table S6 and S7 provide diffe...

Additional file 2: of Evidence from genome wide association studies implicates reduced control of Epstein-Barr virus infection in multiple sclerosis susceptibility

Ali Afrasiabi (6652580)
Grant Parnell (228200)
Nicole Fewings (6652583)
Stephen Schibeci (753421)
Monica Basuki (787103)
Ramya Chandramohan (6652586)
Yuan Zhou (179597)
Bruce Taylor (4417426)
David Brown (71846)
Sanjay Swaminathan (392322)
Fiona McKay (753423)
Graeme Stewart (208243)
David Booth (228203)

April 2019

Figure S1. eQTL data of MS risk variants in whole blood (A) and LCLs (B). Figure S2. Identifying gen...

Additional file 3: Table S2. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio GarcĂa (4411630)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Results of differential expression analysis on RNA-seq data. Features are defined in the GTF file in...

Additional file 6: of T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients

Miranda Houtman (5700545)
Louise Ekholm (5567462)
Espen Hesselberg (5700548)
Karine Chemin (221751)
Vivianne Malmström (4151)
Ann Reed (5700551)
Ingrid Lundberg (3497318)
Leonid Padyukov (39206)

August 2018

Differentially expressed genes in CD4+ T cells of HLA-DRB1*03-positive and -negative myositis patien...

Additional file 3: of Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

Amanda McGovern (123689)
Stefan Schoenfelder (115930)
Paul Martin (7160)
Jonathan Massey (283320)
Kate Duffus (3353354)
Darren Plant (176475)
Annie Yarwood (3353351)
Arthur Pratt (3491927)
Amy Anderson (3491921)
John Isaacs (840151)
Julie Diboll (3491924)
Nishanthi Thalayasingam (3491918)
Caroline Ospelt (3366500)
Anne Barton (23499)
Jane Worthington (23502)
Peter Fraser (32141)
Stephen Eyre (424544)
Gisela Orozco (3353348)

November 2016

Contains the normalised expression values for CD4+ T-cells obtained from NRHV participants. (TXT 26 ...

Additional file 2: Figures S1âS14. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio GarcĂa (4411630)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Figure S1. Comparison of longer and shorter CD4+ T cell activation timecourses. Figure S2. Summary d...

Additional file 1: Table S1. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio GarcĂa (4411630)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Gene modules inferred from WGCNA analysis of microarray time-course. Expression fold changes and ass...

Additional file 2: of Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Ana Márquez (467807)
Martin Kerick (234936)
Alexandra Zhernakova (102388)
Javier Gutierrez-Achury (6109181)
Wei-Min Chen (110472)
Suna Onengut-Gumuscu (282049)
Isidoro González-Álvaro (118679)
Luis Rodriguez-Rodriguez (430986)
Raquel Rios-Fernández (6109184)
Miguel González-Gay (3587198)
Maureen Mayes (3464129)
Soumya Raychaudhuri (229153)
Stephen Rich (4035059)
Cisca Wijmenga (32954)
Javier Martín (2584444)

December 2018

Table S3. Results of the subset-based meta-analysis for the lead variants showing evidence of opposi...

Additional file 7: of Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network

Arianne Richard (3412289)
James Peters (3412283)
James Lee (212552)
Golnaz Vahedi (394496)
Alejandro SchĂ¤ffer (3412292)
Richard Siegel (3412286)
Paul Lyons (18632)
Kenneth Smith (149075)

July 2016

The best-associated SNP is listed for each cis-eQTL (FDR <Â 0.1). Studies that have previously ident...

Additional file 9: Table S7a. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio García (760108)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Autoimmune disease COGS gene prioritisation. Overall COGS gene scores (COGS_Overall_Gene_Score) for ...

Additional file 1: of The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Matzaraki, Vasiliki
Magadi Gopalaiah, Vinod Kumar
Wijmenga, Cisca
Zhernakova, Sasha
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Translational Immunology Groningen (TRIGR)

April 2017

Imputed MHC classic alleles and amino acids for infectious diseases. (XLSX 40 kb

Additional file 1: of Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Ana Márquez (467807)
Martin Kerick (234936)
Alexandra Zhernakova (102388)
Javier Gutierrez-Achury (6109181)
Wei-Min Chen (110472)
Suna Onengut-Gumuscu (282049)
Isidoro González-Álvaro (118679)
Luis Rodriguez-Rodriguez (430986)
Raquel Rios-Fernández (6109184)
Miguel González-Gay (3587198)
Maureen Mayes (3464129)
Soumya Raychaudhuri (229153)
Stephen Rich (4035059)
Cisca Wijmenga (32954)
Javier Martín (2584444)

December 2018

Table S1. Case/control datasets included in the study. Table S2. Loci reaching genome-wide level of ...

Additional file 2: Table S2. of Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease

M. Olsson (3585725)
M. Kierczak (3585737)
Å. Karlsson (3585746)
J. Jabłońska (3585731)
P. Leegwater (3585713)
M. Koltookian (3585728)
J. Abadie (3585722)
C. De Citres (3585734)
A. Thomas (2264929)
Å. Hedhammar (3585740)
L. Tintle (3585716)
K. Lindblad-Toh (3585743)
J. Meadows (3585719)

April 2016

Phenotypic overlap observed within the genetic test cohort. Table S3. Primers and Probes used in ana...

Additional file 1 of Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses

van Deuren, Rosanne C.
Arts, Peer
Cavalli, Giulio
Jaeger, Martin
Steehouwer, Marloes
van de Vorst, Maartje
Gilissen, Christian
Joosten, Leo A. B.
Dinarello, Charles A.
Mhlanga, Musa M.
Magadi Gopalaiah, Vinod Kumar
Netea, Mihai G.
van de Veerdonk, Frank L.
Hoischen, Alexander
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
University of Colorado

May 2021

Additional file 1: Supplementary Tables. Table S1. Variant grouping strategies of 48 Interleukin-1 p...

Additional file 1: of Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci

Jared Dean (3288975)
Ryan Emerson (2591968)
Marissa Vignali (482139)
Anna Sherwood (3289119)
Mark Rieder (44223)
Christopher Carlson (707407)
Harlan Robins (88134)

November 2015

Table listing the number of sequences observed in the study (including total, unique, productive, an...

Additional file 2: of T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients

Miranda Houtman (5700545)
Louise Ekholm (5567462)
Espen Hesselberg (5700548)
Karine Chemin (221751)
Vivianne Malmström (4151)
Ann Reed (5700551)
Ingrid Lundberg (3497318)
Leonid Padyukov (39206)

August 2018

Differentially expressed genes for CD4+ T cells of PM and DM patients. Table S6 and S7 provide diffe...

Additional file 2: of Evidence from genome wide association studies implicates reduced control of Epstein-Barr virus infection in multiple sclerosis susceptibility

Ali Afrasiabi (6652580)
Grant Parnell (228200)
Nicole Fewings (6652583)
Stephen Schibeci (753421)
Monica Basuki (787103)
Ramya Chandramohan (6652586)
Yuan Zhou (179597)
Bruce Taylor (4417426)
David Brown (71846)
Sanjay Swaminathan (392322)
Fiona McKay (753423)
Graeme Stewart (208243)
David Booth (228203)

April 2019

Figure S1. eQTL data of MS risk variants in whole blood (A) and LCLs (B). Figure S2. Identifying gen...

Additional file 3: Table S2. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Oliver Burren (4411639)
Arcadio Rubio GarcĂa (4411630)
Biola-Maria Javierre (3432176)
Daniel Rainbow (4411645)
Jonathan Cairns (3432167)
Nicholas Cooper (4318762)
John Lambourne (4411627)
Ellen Schofield (4411654)
Xaquin Castro Dopico (4411636)
Ricardo Ferreira (4411642)
Richard Coulson (4330936)
Frances Burden (4411648)
Sophia Rowlston (4411651)
Kate Downes (242215)
Steven Wingett (3432179)
Mattia Frontini (747672)
Willem Ouwehand (269630)
Peter Fraser (32141)
Mikhail Spivakov (47286)
John Todd (317993)
Linda Wicker (4411657)
Antony Cutler (4411633)
Chris Wallace (210182)

September 2017

Results of differential expression analysis on RNA-seq data. Features are defined in the GTF file in...

Additional file 6: of T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients

Miranda Houtman (5700545)
Louise Ekholm (5567462)
Espen Hesselberg (5700548)
Karine Chemin (221751)
Vivianne Malmström (4151)
Ann Reed (5700551)
Ingrid Lundberg (3497318)
Leonid Padyukov (39206)

August 2018

Differentially expressed genes in CD4+ T cells of HLA-DRB1*03-positive and -negative myositis patien...

Additional file 2: of Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

Abstract

Extracted data

Additional file 2: of Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

Abstract

Extracted data

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