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

Number of SNPs per method in RNA-seq data.

Emma M. Quinn (394306)
Paul Cormican (147333)
Elaine M. Kenny (394307)
Matthew Hill (394308)
Richard Anney (394309)
Michael Gill (195307)
Aiden P. Corvin (195303)
Derek W. Morris (147340)

March 2013

This figure displays the number of SNPs called for each of the 8 methods used. The proportion of ...

RNA seq klar vs Wt all genes count.

Marcus D. Kilwein (16828051)
T. Kim Dao (16828054)
Michael A. Welte (8339487)

August 2023

The counts for the genes detected in klar-/- and wild type. The columns from left to right show the ...

Trend in effects associated with regulatory classes of intergenic cis-eQTLs.

Maiko Narahara (582213)
Koichiro Higasa (23926)
Seiji Nakamura (126240)
Yasuharu Tabara (344614)
Takahisa Kawaguchi (158644)
Miho Ishii (389751)
Kenichi Matsubara (22850)
Fumihiko Matsuda (137136)
Ryo Yamada (8761)

June 2014

The box-and-whisker plots show distributions of |β| values (A) or of R2 values ...

The number of detected cis-eQTLs is dependent on the expression levels of the transcripts.

Vinod Kumar (48743)
Harm-Jan Westra (102374)
Juha Karjalainen (102376)
Daria V. Zhernakova (102377)
Tõnu Esko (102379)
Barbara Hrdlickova (102382)
Rodrigo Almeida (102386)
Alexandra Zhernakova (102388)
Eva Reinmaa (102391)
Urmo Võsa (102394)
Marten H. Hofker (102396)
Rudolf S. N. Fehrmann (87558)
Jingyuan Fu (102399)
Sebo Withoff (102402)
Andres Metspalu (61760)
Lude Franke (102406)
Cisca Wijmenga (32954)

January 2013

(A) Quantile-normalized average expression intensity and (B) number of cis-eQTL affected p...

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

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 cis-regulated tags mapping to different genomic regions in tag-wise DeepSAGE eQT...

Summary statistics and counts of cis- and trans-eQTLs at thresholds by R2 or |β|.

Maiko Narahara (582213)
Koichiro Higasa (23926)
Seiji Nakamura (126240)
Yasuharu Tabara (344614)
Takahisa Kawaguchi (158644)
Miho Ishii (389751)
Kenichi Matsubara (22850)
Fumihiko Matsuda (137136)
Ryo Yamada (8761)

June 2014

FDR: false discovery rate; FWER: family-wise error rate; SD: standard deviation; IQR: inter-quart...

Fraction of shared cis-eQTLs at 10% FDR between pairs of various versions of normalized Pickrell RNA-seq data.

Sara Mostafavi (51056)
Alexis Battle (434619)
Xiaowei Zhu (24440)
Alexander E. Urban (195065)
Douglas Levinson (318886)
Stephen B. Montgomery (159816)
Daphne Koller (47384)

July 2013

Each row depicts the fraction of cis-eQTLs discovered using a particular normalization method tha...

Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data

Yi-Juan Hu (735313)
Wei Sun (93580)
Jung-Ying Tzeng (714702)
Charles M. Perou (109977)

November 2015

<div>Studies of expression quantitative trait loci (eQTLs) offer insight into the molecular mecha...

Study design.

Frank P. Diekstra (172218)
Christiaan G. J. Saris (172223)
Wouter van Rheenen (172229)
Lude Franke (102406)
Ritsert C. Jansen (32125)
Michael A. van Es (119418)
Paul W. J. van Vught (172235)
Hylke M. Blauw (172237)
Ewout J. N. Groen (172239)
Steve Horvath (28847)
Karol Estrada (149937)
Fernando Rivadeneira (61551)
Albert Hofman (107303)
Andre G. Uitterlinden (89938)
Wim Robberecht (172245)
Peter M. Andersen (172248)
Judith Melki (172253)
Vincent Meininger (136286)
Orla Hardiman (23292)
John E. Landers (172264)
Robert H. Brown Jr. (157813)
Aleksey Shatunov (172270)
Christopher E. Shaw (85395)
P. Nigel Leigh (172275)
Ammar Al-Chalabi (58021)
Roel A. Ophoff (155472)
Leonard H. van den Berg (119440)
Jan H. Veldink (119438)

April 2012

For each step, the number of resulting SNP-transcript pairs in cis is shown.</p

Number of analyzed RNA and DNA sequences in the study (after alignment to Galgal4).

Laure Frésard (747003)
Sophie Leroux (64459)
Pierre-François Roux (464355)
Christophe Klopp (120981)
Stéphane Fabre (153139)
Diane Esquerré (86529)
Patrice Dehais (3585785)
Anis Djari (414687)
David Gourichon (58066)
Sandrine Lagarrigue (214977)
Frédérique Pitel (64462)

May 2015

Number of analyzed RNA and DNA sequences in the study (after alignment to Galgal4).</p

Number of differentially expressed transcripts among the mixes, as identified using various bioinformatics tools and RefSeq+ annotation.

Dena Leshkowitz (420463)
Ester Feldmesser (439160)
Gilgi Friedlander (21025)
Ghil Jona (2622553)
Elena Ainbinder (2622550)
Yisrael Parmet (405601)
Shirley Horn-Saban (66316)

April 2016

Number of differentially expressed transcripts among the mixes, as identified using various bioin...

Number of ORF Extending Variants in RNA-seq Data.

Matthew S. Hestand (439188)
Theodore S. Kalbfleisch (186117)
Stephen J. Coleman (439187)
Zheng Zeng (383660)
Jinze Liu (383649)
Ludovic Orlando (204746)
James N. MacLeod (3286986)

June 2015

Indicated is the number of variants discovered by RNA-seq that extend ORFs of an RNA-seq defined ...

Number of SNPs and relative transcripts in Island population against mainland reference transcriptome.

Martina Trapanese (3251337)
Maria Buglione (3251328)
Valeria Maselli (3251331)
Simona Petrelli (3251340)
Serena Aceto (281495)
Domenico Fulgione (3197028)

September 2017

Number of SNPs and relative transcripts in Island population against mainland reference transcrip...

Number of delRNAs detected in Genbank's human EST database and whole cell transcriptome transcriptome for each systematic nucleotide deletions (k).

Ganesh Warthi (3878926)
Hervé Seligmann (89516)

May 2019

Number of delRNAs detected in Genbank's human EST database and whole cell transcriptome transcriptom...

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated transcripts.

Lucy Mackenzie-Impoinvil (6278108)
Gareth D. Weedall (215713)
Juan C. Lol (6278111)
Jesús Pinto (6278114)
Lucrecia Vizcaino (6278117)
Nicole Dzuris (6278120)
Jacob Riveron (3440567)
Norma Padilla (44896)
Charles Wondji (3419594)
Audrey Lenhart (354002)

January 2019

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated tra...

Number of SNPs per method in RNA-seq data.

Emma M. Quinn (394306)
Paul Cormican (147333)
Elaine M. Kenny (394307)
Matthew Hill (394308)
Richard Anney (394309)
Michael Gill (195307)
Aiden P. Corvin (195303)
Derek W. Morris (147340)

March 2013

This figure displays the number of SNPs called for each of the 8 methods used. The proportion of ...

RNA seq klar vs Wt all genes count.

Marcus D. Kilwein (16828051)
T. Kim Dao (16828054)
Michael A. Welte (8339487)

August 2023

The counts for the genes detected in klar-/- and wild type. The columns from left to right show the ...

Trend in effects associated with regulatory classes of intergenic cis-eQTLs.

Maiko Narahara (582213)
Koichiro Higasa (23926)
Seiji Nakamura (126240)
Yasuharu Tabara (344614)
Takahisa Kawaguchi (158644)
Miho Ishii (389751)
Kenichi Matsubara (22850)
Fumihiko Matsuda (137136)
Ryo Yamada (8761)

June 2014

The box-and-whisker plots show distributions of |β| values (A) or of R2 values ...

The number of detected cis-eQTLs is dependent on the expression levels of the transcripts.

Vinod Kumar (48743)
Harm-Jan Westra (102374)
Juha Karjalainen (102376)
Daria V. Zhernakova (102377)
Tõnu Esko (102379)
Barbara Hrdlickova (102382)
Rodrigo Almeida (102386)
Alexandra Zhernakova (102388)
Eva Reinmaa (102391)
Urmo Võsa (102394)
Marten H. Hofker (102396)
Rudolf S. N. Fehrmann (87558)
Jingyuan Fu (102399)
Sebo Withoff (102402)
Andres Metspalu (61760)
Lude Franke (102406)
Cisca Wijmenga (32954)

January 2013

(A) Quantile-normalized average expression intensity and (B) number of cis-eQTL affected p...

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

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 cis-regulated tags mapping to different genomic regions in tag-wise DeepSAGE eQT...

Summary statistics and counts of cis- and trans-eQTLs at thresholds by R2 or |β|.

Maiko Narahara (582213)
Koichiro Higasa (23926)
Seiji Nakamura (126240)
Yasuharu Tabara (344614)
Takahisa Kawaguchi (158644)
Miho Ishii (389751)
Kenichi Matsubara (22850)
Fumihiko Matsuda (137136)
Ryo Yamada (8761)

June 2014

FDR: false discovery rate; FWER: family-wise error rate; SD: standard deviation; IQR: inter-quart...

Fraction of shared cis-eQTLs at 10% FDR between pairs of various versions of normalized Pickrell RNA-seq data.

Sara Mostafavi (51056)
Alexis Battle (434619)
Xiaowei Zhu (24440)
Alexander E. Urban (195065)
Douglas Levinson (318886)
Stephen B. Montgomery (159816)
Daphne Koller (47384)

July 2013

Each row depicts the fraction of cis-eQTLs discovered using a particular normalization method tha...

Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data

Yi-Juan Hu (735313)
Wei Sun (93580)
Jung-Ying Tzeng (714702)
Charles M. Perou (109977)

November 2015

<div>Studies of expression quantitative trait loci (eQTLs) offer insight into the molecular mecha...

Study design.

Frank P. Diekstra (172218)
Christiaan G. J. Saris (172223)
Wouter van Rheenen (172229)
Lude Franke (102406)
Ritsert C. Jansen (32125)
Michael A. van Es (119418)
Paul W. J. van Vught (172235)
Hylke M. Blauw (172237)
Ewout J. N. Groen (172239)
Steve Horvath (28847)
Karol Estrada (149937)
Fernando Rivadeneira (61551)
Albert Hofman (107303)
Andre G. Uitterlinden (89938)
Wim Robberecht (172245)
Peter M. Andersen (172248)
Judith Melki (172253)
Vincent Meininger (136286)
Orla Hardiman (23292)
John E. Landers (172264)
Robert H. Brown Jr. (157813)
Aleksey Shatunov (172270)
Christopher E. Shaw (85395)
P. Nigel Leigh (172275)
Ammar Al-Chalabi (58021)
Roel A. Ophoff (155472)
Leonard H. van den Berg (119440)
Jan H. Veldink (119438)

April 2012

For each step, the number of resulting SNP-transcript pairs in cis is shown.</p

Number of analyzed RNA and DNA sequences in the study (after alignment to Galgal4).

Laure Frésard (747003)
Sophie Leroux (64459)
Pierre-François Roux (464355)
Christophe Klopp (120981)
Stéphane Fabre (153139)
Diane Esquerré (86529)
Patrice Dehais (3585785)
Anis Djari (414687)
David Gourichon (58066)
Sandrine Lagarrigue (214977)
Frédérique Pitel (64462)

May 2015

Number of analyzed RNA and DNA sequences in the study (after alignment to Galgal4).</p

Number of differentially expressed transcripts among the mixes, as identified using various bioinformatics tools and RefSeq+ annotation.

Dena Leshkowitz (420463)
Ester Feldmesser (439160)
Gilgi Friedlander (21025)
Ghil Jona (2622553)
Elena Ainbinder (2622550)
Yisrael Parmet (405601)
Shirley Horn-Saban (66316)

April 2016

Number of differentially expressed transcripts among the mixes, as identified using various bioin...

Number of ORF Extending Variants in RNA-seq Data.

Matthew S. Hestand (439188)
Theodore S. Kalbfleisch (186117)
Stephen J. Coleman (439187)
Zheng Zeng (383660)
Jinze Liu (383649)
Ludovic Orlando (204746)
James N. MacLeod (3286986)

June 2015

Indicated is the number of variants discovered by RNA-seq that extend ORFs of an RNA-seq defined ...

Number of SNPs and relative transcripts in Island population against mainland reference transcriptome.

Martina Trapanese (3251337)
Maria Buglione (3251328)
Valeria Maselli (3251331)
Simona Petrelli (3251340)
Serena Aceto (281495)
Domenico Fulgione (3197028)

September 2017

Number of SNPs and relative transcripts in Island population against mainland reference transcrip...

Number of delRNAs detected in Genbank's human EST database and whole cell transcriptome transcriptome for each systematic nucleotide deletions (k).

Ganesh Warthi (3878926)
Hervé Seligmann (89516)

May 2019

Number of delRNAs detected in Genbank's human EST database and whole cell transcriptome transcriptom...

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated transcripts.

Lucy Mackenzie-Impoinvil (6278108)
Gareth D. Weedall (215713)
Juan C. Lol (6278111)
Jesús Pinto (6278114)
Lucrecia Vizcaino (6278117)
Nicole Dzuris (6278120)
Jacob Riveron (3440567)
Norma Padilla (44896)
Charles Wondji (3419594)
Audrey Lenhart (354002)

January 2019

Correlation between RNA-Seq and qRT-PCR data of selected genes from the list of the up regulated tra...

Number of SNPs per method in RNA-seq data.

Emma M. Quinn (394306)
Paul Cormican (147333)
Elaine M. Kenny (394307)
Matthew Hill (394308)
Richard Anney (394309)
Michael Gill (195307)
Aiden P. Corvin (195303)
Derek W. Morris (147340)

March 2013

This figure displays the number of SNPs called for each of the 8 methods used. The proportion of ...

RNA seq klar vs Wt all genes count.

Marcus D. Kilwein (16828051)
T. Kim Dao (16828054)
Michael A. Welte (8339487)

August 2023

The counts for the genes detected in klar-/- and wild type. The columns from left to right show the ...

Trend in effects associated with regulatory classes of intergenic cis-eQTLs.

Maiko Narahara (582213)
Koichiro Higasa (23926)
Seiji Nakamura (126240)
Yasuharu Tabara (344614)
Takahisa Kawaguchi (158644)
Miho Ishii (389751)
Kenichi Matsubara (22850)
Fumihiko Matsuda (137136)
Ryo Yamada (8761)

June 2014

The box-and-whisker plots show distributions of |β| values (A) or of R2 values ...

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

Abstract

Extracted data

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

Abstract

Extracted data

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