Additional file 2: of Genome-wide predictors of NF-κB recruitment and transcriptional activity

Marcin Cieślik (3559199)
Stefan Bekiranov (31239)

Publication date

November 2015

DOI

10.6084/m9.figshare.c.3638171_d2.v1

Abstract

NF-κB Target Genes (Gene Name, RefSeq Id, Ensembl Id), log 2 Fold Change (TNF stimulated vs unstimulated), Differential Expression Significance Call (TRUE/FALSE) and NF-κB Peak Detected after TNF Stimulation (TRUE/FALSE) (Data). (CSV 24 kb

Extracted data

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Additional file 2: of Genome-wide predictors of NF-κB recruitment and transcriptional activity

Marcin Cieślik (3559199)
Stefan Bekiranov (31239)

Open link

Publication date

November 2015

DOI

10.6084/m9.figshare.c.3638171_d2.v1

Abstract

Extracted data

Praveen Rajendran (2495365)
Wan-Mohaiza Dashwood (3566624)
Li Li (14993)
Yuki Kang (3566627)
Eunah Kim (3566630)
Gavin Johnson (3566615)
Kay Fischer (3566621)
Christiane Lรถhr (3566636)
David Williams (229939)
Emily Ho (171172)
Masayuki Yamamoto (168116)
David Lieberman (1685806)
Roderick Dashwood (3566618)

September 2015

Gene expression changes in mouse colon. The Table shows gene expression data of '84 genes' in the RT...

Additional file 3: of Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation

Jhuma Pramanik (5894651)
Xi Chen (35903)
Gozde Kar (256068)
Johan Henriksson (462482)
Tomรกs Gomes (5894663)
Jong-Eun Park (231019)
Kedar Natarajan (3563123)
Kerstin Meyer (5894657)
Zhichao Miao (838497)
Andrew McKenzie (522240)
Bidesh Mahata (5894660)
Sarah Teichmann (3553601)

October 2018

Table S2. The list of XBP1 target genes and the genes that are potentially co-regulated by XBP1 and ...

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 1: of NF-κB upregulates glutamine-fructose-6-phosphate transaminase 2 to promote migration in non-small cell lung cancer

Szymon Szymura (6478160)
Jacob Zaemes (6478163)
David Allison (3472163)
Sheena Clift (6478166)
Jaclyn D’Innocenzi (6478169)
Lisa Gray (6478172)
Brian McKenna (2416633)
Benjamin Morris (730923)
Stefan Bekiranov (31239)
Robin LeGallo (6478175)
David Jones (43312)
Marty Mayo (6478178)

March 2019

Is one collated pdf file containing: Table S1. shRNA and siRNA sequences. Table S2. RT-qPCR primer s...

Additional file 2: of RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation

Katarzyna Szołtysek (5956574)
Patryk Janus (5956577)
Gracjana Zając (5956580)
Tomasz Stokowy (5956583)
Anna Walaszczyk (5956586)
Wiesława Widłak (5155094)
Bartosz Wojtaś (5956589)
Bartłomiej Gielniewski (807489)
Simon Cockell (3472001)
Neil Perkins (5956592)
Marek Kimmel (39636)
Piotr Widlak (777996)

November 2018

Table S1. PCR primers; Table S2. Complete set of genes analyzed in the manuscript; Table S3 A GO ter...

Additional file 2: of IFNγ and TNFα synergistically induce apoptosis of mesenchymal stem/stromal cells via the induction of nitric oxide

Xiaolei Li (102381)
Bingxue Shang (6201458)
Ya-nan Li (300741)
Yufang Shi (462173)
Changshun Shao (164939)

January 2019

Figure S2. IFNγ/TNFα induce ER stress in BM-MSCs dependently iNOS activity. (a and b) Both wide type...

Additional file 2: of Inhibition of skin carcinogenesis by suppression of NF-κB dependent ITGAV and TIMP-1 expression in IL-32γ overexpressed condition

Yong Lee (4383514)
Chung Lee (203278)
Jun Bae (6020633)
Kyung Nam (3483323)
Dae Moon (6020636)
Ok Hwang (172719)
Jeong Choi (638146)
Tae Kim (3405566)
Hyoung Jun (6020639)
Young Jung (3426749)
Dae Hwang (3939074)
Sang-Bae Han (2936067)
Do Yoon (3570236)
Jin Hong (758702)

November 2018

Figure S2. Gene network analysis. A and B, The gene map of IL-32 is shown based on known functional ...

Additional file 2: of Gene expression profiling of the human natural killer cell response to Fc receptor activation: unique enhancement in the presence of interleukin-12

Amanda Campbell (2375149)
Kelly Regan (113269)
Neela Bhave (3445943)
Arka Pattanayak (3445937)
Robin Parihar (3445955)
Andrew Stiff (3445946)
Prashant Trikha (79835)
Steven Scoville (3445952)
Sandya Liyanarachchi (2555)
Sri Kondadasula (3445949)
Omkar Lele (3445940)
Ramana Davuluri (427884)
Philip Payne (237866)
William Carson (3445934)

October 2015

2a and 2b are entitled Functional analysis of the genes regulated in NK cells following FcR activati...

Additional file 2: Figure S2. of Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization

Tatyana Kuznetsova (2496532)
Shuang-Yin Wang (3517133)
Nagesha Rao (3517145)
Amit Mandoli (2246752)
Joost Martens (70680)
Nils Rother (3517139)
Aafke Aartse (3517142)
Laszlo Groh (3517136)
Eva Janssen-Megens (228359)
Guoliang Li (131171)
Yijun Ruan (18558)
Colin Logie (176875)
Hendrik Stunnenberg (3423284)

December 2015

Activated p65 induces de novo P300 depositions to latent genomic loci. (A) Pile-up heat map depictin...

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 1: of Inhibition of skin carcinogenesis by suppression of NF-κB dependent ITGAV and TIMP-1 expression in IL-32γ overexpressed condition

Yong Lee (4383514)
Chung Lee (203278)
Jun Bae (6020633)
Kyung Nam (3483323)
Dae Moon (6020636)
Ok Hwang (172719)
Jeong Choi (638146)
Tae Kim (3405566)
Hyoung Jun (6020639)
Young Jung (3426749)
Dae Hwang (3939074)
Sang-Bae Han (2936067)
Do Yoon (3570236)
Jin Hong (758702)

November 2018

Figure S1. IL-32 related disease network. Gene (IL-32)–disease network was analyzed based on the GWA...

Additional file 1: of RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation

Katarzyna Szołtysek (5956574)
Patryk Janus (5956577)
Gracjana Zając (5956580)
Tomasz Stokowy (5956583)
Anna Walaszczyk (5956586)
Wiesława Widłak (5155094)
Bartosz Wojtaś (5956589)
Bartłomiej Gielniewski (807489)
Simon Cockell (3472001)
Neil Perkins (5956592)
Marek Kimmel (39636)
Piotr Widlak (777996)

November 2018

Figure S1. Clonogenic survival of wild-type U2-OS cells exposed to different doses of ionizing radia...

Additional file 5: of Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

Hong Wang (13528)
Yupeng Li (507508)
John Ryder (6092906)
Justin Hole (6092909)
Philip Ebert (6092912)
David Airey (513432)
Hui-Rong Qian (18854)
Benjamin Logsdon (3491201)
Alice Fisher (6092915)
Zeshan Ahmed (6092918)
Tracey Murray (5632871)
Annalisa Cavallini (6092921)
Suchira Bose (6092924)
Brian Eastwood (6092927)
David Collier (231300)
Jeffrey Dage (729068)
Bradley Miller (1869454)
Kalpana Merchant (6092930)
Michael OâNeill (6094406)
Ronald Demattos (6092933)

December 2018

Figure S3. (A). NF-kappa B signaling pathway and (B). AD pathway overlaid with gene expression chang...

Additional file 1: of The inherited variations of a p53-responsive enhancer in 13q12.12 confer lung cancer risk by attenuating TNFRSF19 expression

Lipei Shao (801701)
Xianglin Zuo (6738374)
Yin Yang (35103)
Yu Zhang (12946)
Nan Yang (305078)
Bin Shen (143992)
Jianying Wang (475432)
Xuchun Wang (1467352)
Ruilei Li (6738386)
Guangfu Jin (102661)
Dawei Yu (594337)
Yuan Chen (9740)
Luan Sun (801700)
Zhen Li (49109)
Qiaofen Fu (417712)
Zhibin Hu (102783)
Xiao Han (102316)
Xin Song (465237)
Hongbin Shen (48363)
Yujie Sun (801702)

May 2019

Figure S1. Analysis of H3K4me1 and H3K27ac modifications on the 13q-Enh using ChIP assays in Beas-2B...

Additional file 1: Table S1. of Nrf2 status affects tumor growth, HDAC3 gene promoter associations, and the response to sulforaphane in the colon

Praveen Rajendran (2495365)
Wan-Mohaiza Dashwood (3566624)
Li Li (14993)
Yuki Kang (3566627)
Eunah Kim (3566630)
Gavin Johnson (3566615)
Kay Fischer (3566621)
Christiane Lรถhr (3566636)
David Williams (229939)
Emily Ho (171172)
Masayuki Yamamoto (168116)
David Lieberman (1685806)
Roderick Dashwood (3566618)

September 2015

Gene expression changes in mouse colon. The Table shows gene expression data of '84 genes' in the RT...

Additional file 3: of Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation

Jhuma Pramanik (5894651)
Xi Chen (35903)
Gozde Kar (256068)
Johan Henriksson (462482)
Tomรกs Gomes (5894663)
Jong-Eun Park (231019)
Kedar Natarajan (3563123)
Kerstin Meyer (5894657)
Zhichao Miao (838497)
Andrew McKenzie (522240)
Bidesh Mahata (5894660)
Sarah Teichmann (3553601)

October 2018

Table S2. The list of XBP1 target genes and the genes that are potentially co-regulated by XBP1 and ...

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 1: of NF-κB upregulates glutamine-fructose-6-phosphate transaminase 2 to promote migration in non-small cell lung cancer

Szymon Szymura (6478160)
Jacob Zaemes (6478163)
David Allison (3472163)
Sheena Clift (6478166)
Jaclyn D’Innocenzi (6478169)
Lisa Gray (6478172)
Brian McKenna (2416633)
Benjamin Morris (730923)
Stefan Bekiranov (31239)
Robin LeGallo (6478175)
David Jones (43312)
Marty Mayo (6478178)

March 2019

Is one collated pdf file containing: Table S1. shRNA and siRNA sequences. Table S2. RT-qPCR primer s...

Additional file 2: of RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation

Katarzyna Szołtysek (5956574)
Patryk Janus (5956577)
Gracjana Zając (5956580)
Tomasz Stokowy (5956583)
Anna Walaszczyk (5956586)
Wiesława Widłak (5155094)
Bartosz Wojtaś (5956589)
Bartłomiej Gielniewski (807489)
Simon Cockell (3472001)
Neil Perkins (5956592)
Marek Kimmel (39636)
Piotr Widlak (777996)

November 2018

Table S1. PCR primers; Table S2. Complete set of genes analyzed in the manuscript; Table S3 A GO ter...

Additional file 2: of Inhibition of skin carcinogenesis by suppression of NF-κB dependent ITGAV and TIMP-1 expression in IL-32γ overexpressed condition

Yong Lee (4383514)
Chung Lee (203278)
Jun Bae (6020633)
Kyung Nam (3483323)
Dae Moon (6020636)
Ok Hwang (172719)
Jeong Choi (638146)
Tae Kim (3405566)
Hyoung Jun (6020639)
Young Jung (3426749)
Dae Hwang (3939074)
Sang-Bae Han (2936067)
Do Yoon (3570236)
Jin Hong (758702)

November 2018

Figure S2. Gene network analysis. A and B, The gene map of IL-32 is shown based on known functional ...

Additional file 2: of Gene expression profiling of the human natural killer cell response to Fc receptor activation: unique enhancement in the presence of interleukin-12

Amanda Campbell (2375149)
Kelly Regan (113269)
Neela Bhave (3445943)
Arka Pattanayak (3445937)
Robin Parihar (3445955)
Andrew Stiff (3445946)
Prashant Trikha (79835)
Steven Scoville (3445952)
Sandya Liyanarachchi (2555)
Sri Kondadasula (3445949)
Omkar Lele (3445940)
Ramana Davuluri (427884)
Philip Payne (237866)
William Carson (3445934)

October 2015

2a and 2b are entitled Functional analysis of the genes regulated in NK cells following FcR activati...

Additional file 2: Figure S2. of Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization

Tatyana Kuznetsova (2496532)
Shuang-Yin Wang (3517133)
Nagesha Rao (3517145)
Amit Mandoli (2246752)
Joost Martens (70680)
Nils Rother (3517139)
Aafke Aartse (3517142)
Laszlo Groh (3517136)
Eva Janssen-Megens (228359)
Guoliang Li (131171)
Yijun Ruan (18558)
Colin Logie (176875)
Hendrik Stunnenberg (3423284)

December 2015

Activated p65 induces de novo P300 depositions to latent genomic loci. (A) Pile-up heat map depictin...

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 1: of Inhibition of skin carcinogenesis by suppression of NF-κB dependent ITGAV and TIMP-1 expression in IL-32γ overexpressed condition

Yong Lee (4383514)
Chung Lee (203278)
Jun Bae (6020633)
Kyung Nam (3483323)
Dae Moon (6020636)
Ok Hwang (172719)
Jeong Choi (638146)
Tae Kim (3405566)
Hyoung Jun (6020639)
Young Jung (3426749)
Dae Hwang (3939074)
Sang-Bae Han (2936067)
Do Yoon (3570236)
Jin Hong (758702)

November 2018

Figure S1. IL-32 related disease network. Gene (IL-32)–disease network was analyzed based on the GWA...

Additional file 1: of RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation

Katarzyna Szołtysek (5956574)
Patryk Janus (5956577)
Gracjana Zając (5956580)
Tomasz Stokowy (5956583)
Anna Walaszczyk (5956586)
Wiesława Widłak (5155094)
Bartosz Wojtaś (5956589)
Bartłomiej Gielniewski (807489)
Simon Cockell (3472001)
Neil Perkins (5956592)
Marek Kimmel (39636)
Piotr Widlak (777996)

November 2018

Figure S1. Clonogenic survival of wild-type U2-OS cells exposed to different doses of ionizing radia...

Additional file 5: of Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

Hong Wang (13528)
Yupeng Li (507508)
John Ryder (6092906)
Justin Hole (6092909)
Philip Ebert (6092912)
David Airey (513432)
Hui-Rong Qian (18854)
Benjamin Logsdon (3491201)
Alice Fisher (6092915)
Zeshan Ahmed (6092918)
Tracey Murray (5632871)
Annalisa Cavallini (6092921)
Suchira Bose (6092924)
Brian Eastwood (6092927)
David Collier (231300)
Jeffrey Dage (729068)
Bradley Miller (1869454)
Kalpana Merchant (6092930)
Michael OâNeill (6094406)
Ronald Demattos (6092933)

December 2018

Figure S3. (A). NF-kappa B signaling pathway and (B). AD pathway overlaid with gene expression chang...

Additional file 1: of The inherited variations of a p53-responsive enhancer in 13q12.12 confer lung cancer risk by attenuating TNFRSF19 expression

Lipei Shao (801701)
Xianglin Zuo (6738374)
Yin Yang (35103)
Yu Zhang (12946)
Nan Yang (305078)
Bin Shen (143992)
Jianying Wang (475432)
Xuchun Wang (1467352)
Ruilei Li (6738386)
Guangfu Jin (102661)
Dawei Yu (594337)
Yuan Chen (9740)
Luan Sun (801700)
Zhen Li (49109)
Qiaofen Fu (417712)
Zhibin Hu (102783)
Xiao Han (102316)
Xin Song (465237)
Hongbin Shen (48363)
Yujie Sun (801702)

May 2019

Figure S1. Analysis of H3K4me1 and H3K27ac modifications on the 13q-Enh using ChIP assays in Beas-2B...

Additional file 1: Table S1. of Nrf2 status affects tumor growth, HDAC3 gene promoter associations, and the response to sulforaphane in the colon

Praveen Rajendran (2495365)
Wan-Mohaiza Dashwood (3566624)
Li Li (14993)
Yuki Kang (3566627)
Eunah Kim (3566630)
Gavin Johnson (3566615)
Kay Fischer (3566621)
Christiane Lรถhr (3566636)
David Williams (229939)
Emily Ho (171172)
Masayuki Yamamoto (168116)
David Lieberman (1685806)
Roderick Dashwood (3566618)

September 2015

Gene expression changes in mouse colon. The Table shows gene expression data of '84 genes' in the RT...

Additional file 3: of Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation

Jhuma Pramanik (5894651)
Xi Chen (35903)
Gozde Kar (256068)
Johan Henriksson (462482)
Tomรกs Gomes (5894663)
Jong-Eun Park (231019)
Kedar Natarajan (3563123)
Kerstin Meyer (5894657)
Zhichao Miao (838497)
Andrew McKenzie (522240)
Bidesh Mahata (5894660)
Sarah Teichmann (3553601)

October 2018

Table S2. The list of XBP1 target genes and the genes that are potentially co-regulated by XBP1 and ...

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 Genome-wide predictors of NF-κB recruitment and transcriptional activity

Abstract

Extracted data

Additional file 2: of Genome-wide predictors of NF-κB recruitment and transcriptional activity

Abstract

Extracted data

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