Number of cis-regulated tags mapping to different genomic regions in tag-wise DeepSAGE eQTL mapping.

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods

Li, Yifeng
Shi, Wenqiang
Wasserman, Wyeth W

May 2018

Background: In the human genome, 98% of DNA sequences are non-protein-coding region...

List of genes regulated by each one of the 11 trans-regulatory hotspots regions.

Angela Cánovas (168984)
Ramona N. Pena (168986)
David Gallardo (168988)
Oscar Ramírez (168989)
Marcel Amills (168991)
Raquel Quintanilla (168993)

April 2012

List of genes regulated by each one of the 11 trans-regulatory hotspots regions.</p

Distribution of genome-wide expression QTL amongst pig chromosomes.

Angela Cánovas (168984)
Ramona N. Pena (168986)
David Gallardo (168988)
Oscar Ramírez (168989)
Marcel Amills (168991)
Raquel Quintanilla (168993)

April 2012

(A) Total number of eQTL and (B) cis-acting (▪) and trans-acting (▴) eQTL.</p

The number of cis-regulated tags per gene.

Daria V. Zhernakova (102377)
Eleonora de Klerk (424575)
Harm-Jan Westra (102374)
Anastasios Mastrokolias (424576)
Shoaib Amini (424577)
Yavuz Ariyurek (424578)
Rick Jansen (198642)
Brenda W. Penninx (238627)
Jouke J. Hottenga (424579)
Gonneke Willemsen (75573)
Eco J. de Geus (179549)
Dorret I. Boomsma (109746)
Jan H. Veldink (119438)
Leonard H. van den Berg (119440)
Cisca Wijmenga (32954)
Johan T. den Dunnen (184378)
Gert-Jan B. van Ommen (197915)
Peter A. C. 't Hoen (168822)
Lude Franke (102406)

June 2013

The percentages of cis-regulated tags mapping into the same gene are indicated (781 genes overall...

Number of detected cis-eQTLs in transcript-wise analysis of three harmonized RNA NGS datasets.

Daria V. Zhernakova (102377)
Eleonora de Klerk (424575)
Harm-Jan Westra (102374)
Anastasios Mastrokolias (424576)
Shoaib Amini (424577)
Yavuz Ariyurek (424578)
Rick Jansen (198642)
Brenda W. Penninx (238627)
Jouke J. Hottenga (424579)
Gonneke Willemsen (75573)
Eco J. de Geus (179549)
Dorret I. Boomsma (109746)
Jan H. Veldink (119438)
Leonard H. van den Berg (119440)
Cisca Wijmenga (32954)
Johan T. den Dunnen (184378)
Gert-Jan B. van Ommen (197915)
Peter A. C. 't Hoen (168822)
Lude Franke (102406)

June 2013

Number of detected cis-eQTLs in transcript-wise analysis of three harmonized RNA NGS datas...

The uneven distributions of the regulated target genes.

Wensheng Zhang (41833)
Andrea Edwards (154654)
Erik K. Flemington (154656)
Kun Zhang (108291)

October 2013

In drawing the plots, cis- located eQTL (sQTL) genes (regulators) are ordered by the numbers of t...

Cis-regulating SNPs significantly* affecting multiple tags of the same gene in opposite directions.

Daria V. Zhernakova (102377)
Eleonora de Klerk (424575)
Harm-Jan Westra (102374)
Anastasios Mastrokolias (424576)
Shoaib Amini (424577)
Yavuz Ariyurek (424578)
Rick Jansen (198642)
Brenda W. Penninx (238627)
Jouke J. Hottenga (424579)
Gonneke Willemsen (75573)
Eco J. de Geus (179549)
Dorret I. Boomsma (109746)
Jan H. Veldink (119438)
Leonard H. van den Berg (119440)
Cisca Wijmenga (32954)
Johan T. den Dunnen (184378)
Gert-Jan B. van Ommen (197915)
Peter A. C. 't Hoen (168822)
Lude Franke (102406)

June 2013

*Only significant eQTLs with FDR<0.05 for both cis-regulated tags were used.</p

eQTL SNPs are enriched within activating cis-regulatory elements.

Christopher D. Brown (219934)
Lara M. Mangravite (121414)
Barbara E. Engelhardt (139657)

August 2013

(A–I) CAP_LCL eQTL SNP () overlap with predicted cis-regulatory elements. Each row of panels depi...

Number of DEGs in the different genotypes.

Jing Wu (54032)
Lanfen Wang (185188)
Long Li (6555)
Shumin Wang (402967)

October 2014

The numbers of DEGs that were exclusively up- or down-regulated in one genotype are shown in each...

Distributions of DAFs of all variants, analyzed variants, cis-eQTLs, and trans-eQTLs in gene regions.

Leeyoung Park (131449)

December 2016

Distributions of DAFs of all variants, analyzed variants, cis-eQTLs, and trans-eQTLs in gene regi...

a–d): eQTLs with simultaneous impact on expression levels of at least five genes in trans.

Katharina Schramm (528479)
Carola Marzi (236979)
Claudia Schurmann (112694)
Maren Carstensen (112706)
Eva Reinmaa (102391)
Reiner Biffar (135695)
Gertrud Eckstein (552976)
Christian Gieger (87555)
Hans-Jörgen Grabe (552977)
Georg Homuth (110202)
Gabriele Kastenmüller (552978)
Reedik Mägi (667294)
Andres Metspalu (61760)
Evelin Mihailov (419003)
Annette Peters (62601)
Astrid Petersmann (552979)
Michael Roden (73251)
Konstantin Strauch (73658)
Karsten Suhre (67967)
Alexander Teumer (112757)
Uwe Völker (112748)
Henry Völzke (64286)
Rui Wang-Sattler (36841)
Melanie Waldenberger (236985)
Thomas Meitinger (26605)
Thomas Illig (44906)
Christian Herder (44905)
Harald Grallert (72666)
Holger Prokisch (26590)

April 2014

a) Chromosome 12. The eQTL was located upstream of lysozyme (LYZ), a gene residing ...

Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).

Angela Cánovas (168984)
Ramona N. Pena (168986)
David Gallardo (168988)
Oscar Ramírez (168989)
Marcel Amills (168991)
Raquel Quintanilla (168993)

April 2012

Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).</p

The locations of all mapped eQTL.

Elizabeth G. King (561675)
Brian J. Sanderson (561676)
Casey L. McNeil (561677)
Anthony D. Long (207329)
Stuart J. Macdonald (561678)

May 2014

The location of the transcripts whose expression measures are mapped are along the x axis and the...

Characterization of trans-associations.

Kibaick Lee (280272)
Sang Cheol Kim (137613)
Inkyung Jung (94394)
Kwoneel Kim (280273)
Jungmin Seo (225417)
Heun-Sik Lee (186229)
Gireesh K. Bogu (172997)
Dongsup Kim (50568)
Sanghyuk Lee (6060)
Byungwook Lee (23910)
Jung Kyoon Choi (225420)

February 2013

(A) The number of trans-regulatory loci associated with each chromatin trait (left) and ge...

Mapping results of all the SNPs researched.

Lingtao Su (701306)
Guixia Liu (151574)
Han Wang (254423)
Yuan Tian (225002)
Zhihui Zhou (701307)
Liang Han (339956)
Lun Yan (701308)

March 2015

All: the number of SNPs considered; On Gene: the number of SNPs mapped on genes; Between Gene: th...

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods

Li, Yifeng
Shi, Wenqiang
Wasserman, Wyeth W

May 2018

Background: In the human genome, 98% of DNA sequences are non-protein-coding region...

List of genes regulated by each one of the 11 trans-regulatory hotspots regions.

Angela Cánovas (168984)
Ramona N. Pena (168986)
David Gallardo (168988)
Oscar Ramírez (168989)
Marcel Amills (168991)
Raquel Quintanilla (168993)

April 2012

List of genes regulated by each one of the 11 trans-regulatory hotspots regions.</p

Distribution of genome-wide expression QTL amongst pig chromosomes.

Angela Cánovas (168984)
Ramona N. Pena (168986)
David Gallardo (168988)
Oscar Ramírez (168989)
Marcel Amills (168991)
Raquel Quintanilla (168993)

April 2012

(A) Total number of eQTL and (B) cis-acting (▪) and trans-acting (▴) eQTL.</p

The number of cis-regulated tags per gene.

Daria V. Zhernakova (102377)
Eleonora de Klerk (424575)
Harm-Jan Westra (102374)
Anastasios Mastrokolias (424576)
Shoaib Amini (424577)
Yavuz Ariyurek (424578)
Rick Jansen (198642)
Brenda W. Penninx (238627)
Jouke J. Hottenga (424579)
Gonneke Willemsen (75573)
Eco J. de Geus (179549)
Dorret I. Boomsma (109746)
Jan H. Veldink (119438)
Leonard H. van den Berg (119440)
Cisca Wijmenga (32954)
Johan T. den Dunnen (184378)
Gert-Jan B. van Ommen (197915)
Peter A. C. 't Hoen (168822)
Lude Franke (102406)

June 2013

The percentages of cis-regulated tags mapping into the same gene are indicated (781 genes overall...

Number of detected cis-eQTLs in transcript-wise analysis of three harmonized RNA NGS datasets.

Daria V. Zhernakova (102377)
Eleonora de Klerk (424575)
Harm-Jan Westra (102374)
Anastasios Mastrokolias (424576)
Shoaib Amini (424577)
Yavuz Ariyurek (424578)
Rick Jansen (198642)
Brenda W. Penninx (238627)
Jouke J. Hottenga (424579)
Gonneke Willemsen (75573)
Eco J. de Geus (179549)
Dorret I. Boomsma (109746)
Jan H. Veldink (119438)
Leonard H. van den Berg (119440)
Cisca Wijmenga (32954)
Johan T. den Dunnen (184378)
Gert-Jan B. van Ommen (197915)
Peter A. C. 't Hoen (168822)
Lude Franke (102406)

June 2013

Number of detected cis-eQTLs in transcript-wise analysis of three harmonized RNA NGS datas...

The uneven distributions of the regulated target genes.

Wensheng Zhang (41833)
Andrea Edwards (154654)
Erik K. Flemington (154656)
Kun Zhang (108291)

October 2013

In drawing the plots, cis- located eQTL (sQTL) genes (regulators) are ordered by the numbers of t...

Cis-regulating SNPs significantly* affecting multiple tags of the same gene in opposite directions.

Daria V. Zhernakova (102377)
Eleonora de Klerk (424575)
Harm-Jan Westra (102374)
Anastasios Mastrokolias (424576)
Shoaib Amini (424577)
Yavuz Ariyurek (424578)
Rick Jansen (198642)
Brenda W. Penninx (238627)
Jouke J. Hottenga (424579)
Gonneke Willemsen (75573)
Eco J. de Geus (179549)
Dorret I. Boomsma (109746)
Jan H. Veldink (119438)
Leonard H. van den Berg (119440)
Cisca Wijmenga (32954)
Johan T. den Dunnen (184378)
Gert-Jan B. van Ommen (197915)
Peter A. C. 't Hoen (168822)
Lude Franke (102406)

June 2013

*Only significant eQTLs with FDR<0.05 for both cis-regulated tags were used.</p

eQTL SNPs are enriched within activating cis-regulatory elements.

Christopher D. Brown (219934)
Lara M. Mangravite (121414)
Barbara E. Engelhardt (139657)

August 2013

(A–I) CAP_LCL eQTL SNP () overlap with predicted cis-regulatory elements. Each row of panels depi...

Number of DEGs in the different genotypes.

Jing Wu (54032)
Lanfen Wang (185188)
Long Li (6555)
Shumin Wang (402967)

October 2014

The numbers of DEGs that were exclusively up- or down-regulated in one genotype are shown in each...

Distributions of DAFs of all variants, analyzed variants, cis-eQTLs, and trans-eQTLs in gene regions.

Leeyoung Park (131449)

December 2016

Distributions of DAFs of all variants, analyzed variants, cis-eQTLs, and trans-eQTLs in gene regi...

a–d): eQTLs with simultaneous impact on expression levels of at least five genes in trans.

Katharina Schramm (528479)
Carola Marzi (236979)
Claudia Schurmann (112694)
Maren Carstensen (112706)
Eva Reinmaa (102391)
Reiner Biffar (135695)
Gertrud Eckstein (552976)
Christian Gieger (87555)
Hans-Jörgen Grabe (552977)
Georg Homuth (110202)
Gabriele Kastenmüller (552978)
Reedik Mägi (667294)
Andres Metspalu (61760)
Evelin Mihailov (419003)
Annette Peters (62601)
Astrid Petersmann (552979)
Michael Roden (73251)
Konstantin Strauch (73658)
Karsten Suhre (67967)
Alexander Teumer (112757)
Uwe Völker (112748)
Henry Völzke (64286)
Rui Wang-Sattler (36841)
Melanie Waldenberger (236985)
Thomas Meitinger (26605)
Thomas Illig (44906)
Christian Herder (44905)
Harald Grallert (72666)
Holger Prokisch (26590)

April 2014

a) Chromosome 12. The eQTL was located upstream of lysozyme (LYZ), a gene residing ...

Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).

Angela Cánovas (168984)
Ramona N. Pena (168986)
David Gallardo (168988)
Oscar Ramírez (168989)
Marcel Amills (168991)
Raquel Quintanilla (168993)

April 2012

Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).</p

The locations of all mapped eQTL.

Elizabeth G. King (561675)
Brian J. Sanderson (561676)
Casey L. McNeil (561677)
Anthony D. Long (207329)
Stuart J. Macdonald (561678)

May 2014

The location of the transcripts whose expression measures are mapped are along the x axis and the...

Characterization of trans-associations.

Kibaick Lee (280272)
Sang Cheol Kim (137613)
Inkyung Jung (94394)
Kwoneel Kim (280273)
Jungmin Seo (225417)
Heun-Sik Lee (186229)
Gireesh K. Bogu (172997)
Dongsup Kim (50568)
Sanghyuk Lee (6060)
Byungwook Lee (23910)
Jung Kyoon Choi (225420)

February 2013

(A) The number of trans-regulatory loci associated with each chromatin trait (left) and ge...

Mapping results of all the SNPs researched.

Lingtao Su (701306)
Guixia Liu (151574)
Han Wang (254423)
Yuan Tian (225002)
Zhihui Zhou (701307)
Liang Han (339956)
Lun Yan (701308)

March 2015

All: the number of SNPs considered; On Gene: the number of SNPs mapped on genes; Between Gene: th...

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods

Li, Yifeng
Shi, Wenqiang
Wasserman, Wyeth W

May 2018

Background: In the human genome, 98% of DNA sequences are non-protein-coding region...

List of genes regulated by each one of the 11 trans-regulatory hotspots regions.

Angela Cánovas (168984)
Ramona N. Pena (168986)
David Gallardo (168988)
Oscar Ramírez (168989)
Marcel Amills (168991)
Raquel Quintanilla (168993)

April 2012

List of genes regulated by each one of the 11 trans-regulatory hotspots regions.</p

Distribution of genome-wide expression QTL amongst pig chromosomes.

Angela Cánovas (168984)
Ramona N. Pena (168986)
David Gallardo (168988)
Oscar Ramírez (168989)
Marcel Amills (168991)
Raquel Quintanilla (168993)

April 2012

(A) Total number of eQTL and (B) cis-acting (▪) and trans-acting (▴) eQTL.</p

Number of <i>cis-</i>regulated tags mapping to different genomic regions in tag-wise DeepSAGE eQTL mapping.

Abstract

Extracted data

Topics

Number of <i>cis-</i>regulated tags mapping to different genomic regions in tag-wise DeepSAGE eQTL mapping.

Abstract

Extracted data

Topics

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