Additional file 10: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

Open link

Publication date

July 2016

DOI

10.6084/m9.figshare.c.3595976_d10.v1

Abstract

Correlation matrixes of signature scores of core genes for TCZ (a) and ABT (b). (PDF 297 kb

Extracted data

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Data Protection

Additional file 10: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

Open link

Publication date

July 2016

DOI

10.6084/m9.figshare.c.3595976_d10.v1

Abstract

Correlation matrixes of signature scores of core genes for TCZ (a) and ABT (b). (PDF 297 kb

Extracted data

C. Derambure (4048354)
G. Dzangue-Tchoupou (4048339)
C. Berard (4048342)
N. Vergne (4048351)
M. Hiron (4048357)
M. DâAgostino (4048426)
P. Musette (4048333)
O. Vittecoq (4048348)
T. LequerrĂŠ (4048423)

May 2017

Ineffectiveness of 87 mRNA associated with response to ABA/MTX to predict response to adalimumab or ...

Additional file 2: Figure S1. of Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis

Klementy Shchetynsky (3710995)
Lina-Marcella Diaz-Gallo (3710998)
Lasse Folkersen (109487)
Aase Hensvold (3505412)
Anca Catrina (246690)
Louise Berg (54461)
Lars Klareskog (4149)
Leonid Padyukov (39206)

February 2017

Schematic representation of the study workflow. Out of the initial set of genes in direct proximity ...

Validation study of existing gene expression signatures for anti-TNF treatment in patients with rheumatoid arthritis

Toonen, E.J.M.
Gilissen, C.F.
Franke, B.
Kievit, W.
Eijsbouts, A.M.
Broeder, A. den
Reijmersdal, S.V. van
Veltman, J.A.
Scheffer, H.
Radstake, T.R.
van Riel, P.L.
Barrera, P.
Coenen, M.J.

January 2012

Contains fulltext : 110151.pdf (publisher's version ) (Open Access)So far, there a...

Additional file 1: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

Illustration of the distribution of patients in this observational study. (PDF 223 kb

Additional file 9: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

qRT-PCR results of five core genes of each signature identified from GSEA. (PDF 317 kb

Additional file 1: of Gene expression analysis of vascular pathophysiology related to anti-TNF treatment in rheumatoid arthritis

Szilárd Póliska (3165450)
Timea Besenyei (6590546)
Edit Végh (6590549)
Attila Hamar (6590552)
Anita Pusztai (6590555)
Andrea Váncsa (6590558)
Nóra Bodnár (6590561)
Szilvia Szamosi (4799160)
Mária Csumita (6590564)
György Kerekes (6590570)
Zoltán Szabó (211818)
Zoltán Nagy (2668840)
Gabriella Szűcs (6590573)
Sándor Szántó (38675)
Gábor Zahuczky (215986)
László Nagy (2717482)
Zoltán Szekanecz (38677)

April 2019

Table S1. Association of gene expression profiles with vascular pathophysiology in biologic-naïve RA...

Additional file 1: Table S1. of Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis

Klementy Shchetynsky (3710995)
Lina-Marcella Diaz-Gallo (3710998)
Lasse Folkersen (109487)
Aase Hensvold (3505412)
Anca Catrina (246690)
Louise Berg (54461)
Lars Klareskog (4149)
Leonid Padyukov (39206)

February 2017

Clinical features of studied groups of patients with RA and healthy controls. Table S2 The expressio...

Additional file 4: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Genes over-expressed in poor responders to therapy at baseline. Lists of probe sets differentially e...

Additional file 2: of Gene expression analysis of vascular pathophysiology related to anti-TNF treatment in rheumatoid arthritis

Szilárd Póliska (3165450)
Timea Besenyei (6590546)
Edit Végh (6590549)
Attila Hamar (6590552)
Anita Pusztai (6590555)
Andrea Váncsa (6590558)
Nóra Bodnár (6590561)
Szilvia Szamosi (4799160)
Mária Csumita (6590564)
György Kerekes (6590570)
Zoltán Szabó (211818)
Zoltán Nagy (2668840)
Gabriella Szűcs (6590573)
Sándor Szántó (38675)
Gábor Zahuczky (215986)
László Nagy (2717482)
Zoltán Szekanecz (38677)

April 2019

Table S2. Association of gene expression profiles with clinical and vascular responses upon anti-TNF...

Additional file 3: of Identification of differential co-expressed gene networks in early rheumatoid arthritis achieving sustained drug-free remission after treatment with a tocilizumab-based or methotrexate-based strategy

Xavier Teitsma (3514304)
Johannes Jacobs (3514301)
Michal Mokry (236330)
Michelle Borm (4262875)
Attila PethĂś-Schramm (4262896)
Jacob van Laar (213989)
Johannes Bijlsma (3424766)
Floris Lafeber (2301085)

July 2017

Correlations and corresponding P values between the modules and achieving sustained drug-free remiss...

Additional file 1: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Patients’ characteristics (immunohistochemistry studies on needle arthroscopic biopsies). Characteri...

Additional file 3: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Numbers of probe sets displaying a positive correlation with global disease activity indices and eac...

Additional file 1: of Transcription factor motif enrichment in whole transcriptome analysis identifies STAT4 and BCL6 as the most prominent binding motif in systemic juvenile idiopathic arthritis

Boris HĂźgle (3580769)
Anastasia Schippers (5319707)
Nadine Fischer (3580766)
Kim Ohl (5319695)
Bernd Denecke (202688)
Fabio Ticconi (5319701)
Bas Vastert (5319704)
Ivan Costa (3549209)
Johannes-Peter Haas (2868563)
Klaus Tenbrock (5319698)

May 2018

Table S1. List of regulated genes with fold change (FC) > 2 in patients with active disease (ad) ver...

Additional file 2: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Patients’ characteristics (immunohistochemistry studies on ultrasound (US)-guided biopsies). Charact...

Additional file 2: of Identification of differential co-expressed gene networks in early rheumatoid arthritis achieving sustained drug-free remission after treatment with a tocilizumab-based or methotrexate-based strategy

Xavier Teitsma (3514304)
Johannes Jacobs (3514301)
Michal Mokry (236330)
Michelle Borm (4262875)
Attila PethĂś-Schramm (4262896)
Jacob van Laar (213989)
Johannes Bijlsma (3424766)
Floris Lafeber (2301085)

July 2017

Description of the differentially co-expressed genes in the salmon module (tocilizumab plus methotre...

Additional file 3: of Pre-silencing of genes involved in the electron transport chain (ETC) pathway is associated with responsiveness to abatacept in rheumatoid arthritis

C. Derambure (4048354)
G. Dzangue-Tchoupou (4048339)
C. Berard (4048342)
N. Vergne (4048351)
M. Hiron (4048357)
M. DâAgostino (4048426)
P. Musette (4048333)
O. Vittecoq (4048348)
T. LequerrĂŠ (4048423)

May 2017

Ineffectiveness of 87 mRNA associated with response to ABA/MTX to predict response to adalimumab or ...

Additional file 2: Figure S1. of Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis

Klementy Shchetynsky (3710995)
Lina-Marcella Diaz-Gallo (3710998)
Lasse Folkersen (109487)
Aase Hensvold (3505412)
Anca Catrina (246690)
Louise Berg (54461)
Lars Klareskog (4149)
Leonid Padyukov (39206)

February 2017

Schematic representation of the study workflow. Out of the initial set of genes in direct proximity ...

Validation study of existing gene expression signatures for anti-TNF treatment in patients with rheumatoid arthritis

Toonen, E.J.M.
Gilissen, C.F.
Franke, B.
Kievit, W.
Eijsbouts, A.M.
Broeder, A. den
Reijmersdal, S.V. van
Veltman, J.A.
Scheffer, H.
Radstake, T.R.
van Riel, P.L.
Barrera, P.
Coenen, M.J.

January 2012

Contains fulltext : 110151.pdf (publisher's version ) (Open Access)So far, there a...

Additional file 1: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

Illustration of the distribution of patients in this observational study. (PDF 223 kb

Additional file 9: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

qRT-PCR results of five core genes of each signature identified from GSEA. (PDF 317 kb

Additional file 1: of Gene expression analysis of vascular pathophysiology related to anti-TNF treatment in rheumatoid arthritis

Szilárd Póliska (3165450)
Timea Besenyei (6590546)
Edit Végh (6590549)
Attila Hamar (6590552)
Anita Pusztai (6590555)
Andrea Váncsa (6590558)
Nóra Bodnár (6590561)
Szilvia Szamosi (4799160)
Mária Csumita (6590564)
György Kerekes (6590570)
Zoltán Szabó (211818)
Zoltán Nagy (2668840)
Gabriella Szűcs (6590573)
Sándor Szántó (38675)
Gábor Zahuczky (215986)
László Nagy (2717482)
Zoltán Szekanecz (38677)

April 2019

Table S1. Association of gene expression profiles with vascular pathophysiology in biologic-naïve RA...

Additional file 1: Table S1. of Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis

Klementy Shchetynsky (3710995)
Lina-Marcella Diaz-Gallo (3710998)
Lasse Folkersen (109487)
Aase Hensvold (3505412)
Anca Catrina (246690)
Louise Berg (54461)
Lars Klareskog (4149)
Leonid Padyukov (39206)

February 2017

Clinical features of studied groups of patients with RA and healthy controls. Table S2 The expressio...

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Genes over-expressed in poor responders to therapy at baseline. Lists of probe sets differentially e...

Additional file 2: of Gene expression analysis of vascular pathophysiology related to anti-TNF treatment in rheumatoid arthritis

Szilárd Póliska (3165450)
Timea Besenyei (6590546)
Edit Végh (6590549)
Attila Hamar (6590552)
Anita Pusztai (6590555)
Andrea Váncsa (6590558)
Nóra Bodnár (6590561)
Szilvia Szamosi (4799160)
Mária Csumita (6590564)
György Kerekes (6590570)
Zoltán Szabó (211818)
Zoltán Nagy (2668840)
Gabriella Szűcs (6590573)
Sándor Szántó (38675)
Gábor Zahuczky (215986)
László Nagy (2717482)
Zoltán Szekanecz (38677)

April 2019

Table S2. Association of gene expression profiles with clinical and vascular responses upon anti-TNF...

Xavier Teitsma (3514304)
Johannes Jacobs (3514301)
Michal Mokry (236330)
Michelle Borm (4262875)
Attila PethĂś-Schramm (4262896)
Jacob van Laar (213989)
Johannes Bijlsma (3424766)
Floris Lafeber (2301085)

July 2017

Correlations and corresponding P values between the modules and achieving sustained drug-free remiss...

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Patients’ characteristics (immunohistochemistry studies on needle arthroscopic biopsies). Characteri...

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Numbers of probe sets displaying a positive correlation with global disease activity indices and eac...

Additional file 1: of Transcription factor motif enrichment in whole transcriptome analysis identifies STAT4 and BCL6 as the most prominent binding motif in systemic juvenile idiopathic arthritis

Boris HĂźgle (3580769)
Anastasia Schippers (5319707)
Nadine Fischer (3580766)
Kim Ohl (5319695)
Bernd Denecke (202688)
Fabio Ticconi (5319701)
Bas Vastert (5319704)
Ivan Costa (3549209)
Johannes-Peter Haas (2868563)
Klaus Tenbrock (5319698)

May 2018

Table S1. List of regulated genes with fold change (FC) > 2 in patients with active disease (ad) ver...

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Patients’ characteristics (immunohistochemistry studies on ultrasound (US)-guided biopsies). Charact...

Xavier Teitsma (3514304)
Johannes Jacobs (3514301)
Michal Mokry (236330)
Michelle Borm (4262875)
Attila PethĂś-Schramm (4262896)
Jacob van Laar (213989)
Johannes Bijlsma (3424766)
Floris Lafeber (2301085)

July 2017

Description of the differentially co-expressed genes in the salmon module (tocilizumab plus methotre...

Additional file 3: of Pre-silencing of genes involved in the electron transport chain (ETC) pathway is associated with responsiveness to abatacept in rheumatoid arthritis

C. Derambure (4048354)
G. Dzangue-Tchoupou (4048339)
C. Berard (4048342)
N. Vergne (4048351)
M. Hiron (4048357)
M. DâAgostino (4048426)
P. Musette (4048333)
O. Vittecoq (4048348)
T. LequerrĂŠ (4048423)

May 2017

Ineffectiveness of 87 mRNA associated with response to ABA/MTX to predict response to adalimumab or ...

Additional file 2: Figure S1. of Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis

Klementy Shchetynsky (3710995)
Lina-Marcella Diaz-Gallo (3710998)
Lasse Folkersen (109487)
Aase Hensvold (3505412)
Anca Catrina (246690)
Louise Berg (54461)
Lars Klareskog (4149)
Leonid Padyukov (39206)

February 2017

Schematic representation of the study workflow. Out of the initial set of genes in direct proximity ...

Validation study of existing gene expression signatures for anti-TNF treatment in patients with rheumatoid arthritis

Toonen, E.J.M.
Gilissen, C.F.
Franke, B.
Kievit, W.
Eijsbouts, A.M.
Broeder, A. den
Reijmersdal, S.V. van
Veltman, J.A.
Scheffer, H.
Radstake, T.R.
van Riel, P.L.
Barrera, P.
Coenen, M.J.

January 2012

Contains fulltext : 110151.pdf (publisher's version ) (Open Access)So far, there a...

Additional file 10: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Abstract

Extracted data

Additional file 10: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Abstract

Extracted data

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