Additional file 3: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Additional file 7: of Conserved regulation of RNA processing in somatic cell reprogramming

Alexander Kanitz (121360)
Afzal Syed (6286067)
Keisuke Kaji (403022)
Mihaela Zavolan (16626)

February 2019

Figure S4. Mouse reprogramming time course. As in Figure S3 but data is from mouse embryonic fibrobl...

Additional file 3: of Connecting genetics and gene expression data for target prioritisation and drug repositioning

Enrico Ferrero (298671)
Pankaj Agarwal (191011)

May 2018

Table S3. Drug repositioning hypotheses based on the significance of the overlap between genes genet...

Additional file 3: Table S2. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

Devi Karunakaran (3556769)
Sahar Al Seesi (663330)
Abdul Banday (3556766)
Marybeth Baumgartner (663329)
Anouk Olthof (3556772)
Christopher Lemoine (663332)
Ion MÄndoiu (3552992)
Rahul Kanadia (464434)

August 2016

DAVID analysis output for static and temporal comparisons. DAVID output for genes belonging to bins ...

Additional file 4: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

DAVID Analysis Table of Biological Processes (FDRâ<â0.05) for Up- or Down-regulated DEGs Between...

Additional file 6: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

Table for S1- or S2-specifically Expressed Genes under DMSO Ctl or Jaki-Treatment at S1 or S2. (XLSX...

Additional file 5: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

Table for DEGs listed in Spermatogenesis/Meiotic, Mitotic, and DNA Repair GO-terms That Are Upregula...

Additional file 2: Figure S3. of Time-course transcriptome analysis of human cellular reprogramming from multiple cell types reveals the drastic change occurs between the mid phase and the late phase

Akihiro Kuno (4733382)
Ken Nishimura (445291)
Satoru Takahashi (32871)

January 2018

Epigenetic modification during reprogramming. (a) Gene expression patterns during reprogramming in f...

Additional file 1: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

Schematic representation of the Dlk1-Dio3 region at mouse chromosome 12qF1. The Gtl2-Rian-Mirg lincR...

Additional file 1: Table S1. of A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification

Xin-Ping Xie (4383745)
Yu-Feng Xie (4383742)
Hong-Qiang Wang (475907)

August 2017

List of 1655 genes with a negative jGRP statistic meaning a down-regulation in LUAD tissues relative...

Additional file 3: Figure S1. of Time-course transcriptome analysis of human cellular reprogramming from multiple cell types reveals the drastic change occurs between the mid phase and the late phase

Akihiro Kuno (4733382)
Ken Nishimura (445291)
Satoru Takahashi (32871)

January 2018

PCA and HCA of each cell type by using log2 expression value of all 22,062 genes in GPL14550 platfor...

Additional file 7: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

JAK/STAT3 Activity Is Needed to Activate Pluripotent Loci in Reprogramming. DNA methylation of Nanog...

Additional file 3: of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

Alison Merryweather-Clarke (3577583)
Alex Tipping (3577595)
Abigail Lamikanra (3577586)
Rui Fa (281244)
Basel Abu-Jamous (281243)
Hoi Tsang (3577589)
Lee Carpenter (597733)
Kathryn Robson (530528)
Asoke Nandi (3577592)
David Roberts (71016)

October 2016

Figure S4. Gene expression centroids from the adult FBS erythropoiesis data as depicted in Fig.Â 1B....

Additional File 1:

Claudia Preston (5319473)
Saranya Wyles (5319470)
Santiago Reyes (4039796)
Emily Storm (5319482)
Bruce Eckloff (5319479)
Randolph Faustino (5319476)

May 2018

Table S1. Pathway Enrichment Analysis of Upregulated Genes. Table S2. Pathway Enrichment Analysis of...

Additional file 8: of IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation

Roser Vento-Tormo (3403292)
Carlos Company (3403283)
Javier Rodríguez-Ubreva (3403310)
Lorenzo de la Rica (3403286)
José Urquiza (3403304)
Biola Javierre (3403295)
Radhakrishnan Sabarinathan (244382)
Ana Luque (86391)
Manel Esteller (74345)
Josep Aran (3403289)
Damiana Álvarez-Errico (3403307)
Esteban Ballestar (74333)

January 2016

(A) Surface DC and MAC markers analysed by flow cytometry during DC and MAC differentiation in the p...

Additional file 4: of Conserved regulation of RNA processing in somatic cell reprogramming

Alexander Kanitz (121360)
Afzal Syed (6286067)
Keisuke Kaji (403022)
Mihaela Zavolan (16626)

February 2019

Table of comparisons for differential analyses. The file contains an XLSX spreadsheet describing sam...

Additional file 7: of Conserved regulation of RNA processing in somatic cell reprogramming

Alexander Kanitz (121360)
Afzal Syed (6286067)
Keisuke Kaji (403022)
Mihaela Zavolan (16626)

February 2019

Figure S4. Mouse reprogramming time course. As in Figure S3 but data is from mouse embryonic fibrobl...

Additional file 3: of Connecting genetics and gene expression data for target prioritisation and drug repositioning

Enrico Ferrero (298671)
Pankaj Agarwal (191011)

May 2018

Table S3. Drug repositioning hypotheses based on the significance of the overlap between genes genet...

Additional file 3: Table S2. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

Devi Karunakaran (3556769)
Sahar Al Seesi (663330)
Abdul Banday (3556766)
Marybeth Baumgartner (663329)
Anouk Olthof (3556772)
Christopher Lemoine (663332)
Ion MÄndoiu (3552992)
Rahul Kanadia (464434)

August 2016

DAVID analysis output for static and temporal comparisons. DAVID output for genes belonging to bins ...

Additional file 4: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

DAVID Analysis Table of Biological Processes (FDRâ<â0.05) for Up- or Down-regulated DEGs Between...

Additional file 6: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

Table for S1- or S2-specifically Expressed Genes under DMSO Ctl or Jaki-Treatment at S1 or S2. (XLSX...

Additional file 5: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

Table for DEGs listed in Spermatogenesis/Meiotic, Mitotic, and DNA Repair GO-terms That Are Upregula...

Additional file 2: Figure S3. of Time-course transcriptome analysis of human cellular reprogramming from multiple cell types reveals the drastic change occurs between the mid phase and the late phase

Akihiro Kuno (4733382)
Ken Nishimura (445291)
Satoru Takahashi (32871)

January 2018

Epigenetic modification during reprogramming. (a) Gene expression patterns during reprogramming in f...

Additional file 1: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

Schematic representation of the Dlk1-Dio3 region at mouse chromosome 12qF1. The Gtl2-Rian-Mirg lincR...

Additional file 1: Table S1. of A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification

Xin-Ping Xie (4383745)
Yu-Feng Xie (4383742)
Hong-Qiang Wang (475907)

August 2017

List of 1655 genes with a negative jGRP statistic meaning a down-regulation in LUAD tissues relative...

Additional file 3: Figure S1. of Time-course transcriptome analysis of human cellular reprogramming from multiple cell types reveals the drastic change occurs between the mid phase and the late phase

Akihiro Kuno (4733382)
Ken Nishimura (445291)
Satoru Takahashi (32871)

January 2018

PCA and HCA of each cell type by using log2 expression value of all 22,062 genes in GPL14550 platfor...

Additional file 7: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Ling Wang (56577)
Zongliang Jiang (4916698)
Delun Huang (4916707)
Jingyue Duan (4916695)
Chang Huang (418702)
Shannon Sullivan (27443)
Kaneha Vali (4916701)
Yexuan Yin (4916704)
Ming Zhang (9736)
Jill Wegrzyn (141670)
Xiuchun Tian (628675)
Young Tang (4916710)

March 2018

JAK/STAT3 Activity Is Needed to Activate Pluripotent Loci in Reprogramming. DNA methylation of Nanog...

Additional file 3: of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

Alison Merryweather-Clarke (3577583)
Alex Tipping (3577595)
Abigail Lamikanra (3577586)
Rui Fa (281244)
Basel Abu-Jamous (281243)
Hoi Tsang (3577589)
Lee Carpenter (597733)
Kathryn Robson (530528)
Asoke Nandi (3577592)
David Roberts (71016)

October 2016

Figure S4. Gene expression centroids from the adult FBS erythropoiesis data as depicted in Fig.Â 1B....

Additional File 1:

Claudia Preston (5319473)
Saranya Wyles (5319470)
Santiago Reyes (4039796)
Emily Storm (5319482)
Bruce Eckloff (5319479)
Randolph Faustino (5319476)

May 2018

Table S1. Pathway Enrichment Analysis of Upregulated Genes. Table S2. Pathway Enrichment Analysis of...

Additional file 8: of IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation

Roser Vento-Tormo (3403292)
Carlos Company (3403283)
Javier Rodríguez-Ubreva (3403310)
Lorenzo de la Rica (3403286)
José Urquiza (3403304)
Biola Javierre (3403295)
Radhakrishnan Sabarinathan (244382)
Ana Luque (86391)
Manel Esteller (74345)
Josep Aran (3403289)
Damiana Álvarez-Errico (3403307)
Esteban Ballestar (74333)

January 2016

(A) Surface DC and MAC markers analysed by flow cytometry during DC and MAC differentiation in the p...

Additional file 4: of Conserved regulation of RNA processing in somatic cell reprogramming

Alexander Kanitz (121360)
Afzal Syed (6286067)
Keisuke Kaji (403022)
Mihaela Zavolan (16626)

February 2019

Table of comparisons for differential analyses. The file contains an XLSX spreadsheet describing sam...

Additional file 7: of Conserved regulation of RNA processing in somatic cell reprogramming

Alexander Kanitz (121360)
Afzal Syed (6286067)
Keisuke Kaji (403022)
Mihaela Zavolan (16626)

February 2019

Figure S4. Mouse reprogramming time course. As in Figure S3 but data is from mouse embryonic fibrobl...

Additional file 3: of Connecting genetics and gene expression data for target prioritisation and drug repositioning

Enrico Ferrero (298671)
Pankaj Agarwal (191011)

May 2018

Table S3. Drug repositioning hypotheses based on the significance of the overlap between genes genet...

Additional file 3: Table S2. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

Devi Karunakaran (3556769)
Sahar Al Seesi (663330)
Abdul Banday (3556766)
Marybeth Baumgartner (663329)
Anouk Olthof (3556772)
Christopher Lemoine (663332)
Ion MÄndoiu (3552992)
Rahul Kanadia (464434)

August 2016

DAVID analysis output for static and temporal comparisons. DAVID output for genes belonging to bins ...

Additional file 3: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Abstract

Extracted data

Additional file 3: of JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process

Abstract

Extracted data

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