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Table S8

Wehmas, Leah
Wood, Charles E.
Gagne, Remi
Williams, Andrew
Yauk, Carole
Gosink, Mark M.
Dalmas, Deidre A.
Hao, Ruixin
O'Lone, Raegan
Hester, Susan

Publication date

December 2017

DOI

10.5061/dryad.7c4s5/8

Abstract

Significant differentially expressed genes list from each preservation group overlapping with F

Extracted data

Related items

Differentially expressed gene lists - unfiltered

John E. Collins (207876)
Richard J. White (35897)
Nicole Staudt (60273)
Ian M. Sealy (3719416)
Ian Packham (5473280)
Neha Wali (2205688)
Catherine Tudor (5473265)
Cecilia Mazzeo (5473283)
Angela Green (250894)
Emma Siragher (5473271)
Edward Ryder (145998)
Jacqueline K. White (119191)
Irene Papatheodoru (5473268)
Amy Tang (4337950)
Anja Füllgrabe (3719422)
Konstantinos Billis (650319)
Stefan H. Geyer (6306488)
Wolfgang J. Weninger (5516939)
Antonella Galli (250780)
Myriam Hemberger (93502)
Derek L. Stemple (595950)
Elizabeth Robertson (450547)
James C. Smith (68336)
Timothy Mohun (2940327)
David J. Adams (119198)
Elisabeth M. Busch-Nentwich (3719419)

March 2019

Files of differentially expressed genes (using DESeq2) from different mutant lines.see the README fo...

Number of significant differentially expressed genes within each comparative microarray group (filtered for fold change > 2 and p-value < 0.05).

N. Jumper (3812692)
T. Hodgkinson (3812695)
R. Paus (3812698)
A. Bayat (3812689)

March 2017

<p>Number of significant differentially expressed genes within each comparative microarray group (fi...

List of differentially expressed genes and uncharacterized transcripts (±2 fold change, q<0.05).

Jasmin H. Bavarva (422981)
Hongseok Tae (35265)
Robert E. Settlage (422982)
Harold R. Garner (6157)

June 2013

<p>List of differentially expressed genes and uncharacterized transcripts (±2 fold change, q<0.05).<...

Table containing differential expressed genes (result of edgeR)

Patel, Alok
Dettleff, Phillip
Hernández, Eric
Martinez, Victor

August 2015

This table contains data of list of genes that were < 0.01 FDR value and differed in their expressio...

Table containing differential expressed genes (result of edgeR)

Alok Patel (1408258)
Phillip Dettleff (3362153)
Eric Hernández (3362150)
Victor Martinez (2539555)

November 2016

This table contains data of list of genes that were < 0.01 FDR value and differed in their expressio...

Retrieved differentially expressed genes in CF (adapted from [31]).

Pascal Trouvé (317768)
Emmanuelle Génin (91542)
Claude Férec (204332)

March 2017

<p>The lower part of the table shows genes shared between two or more studies when all six studies a...

List of differentially expressed transcripts that have putative homologs in GenBank.

Si-Ming Zhang (811845)
Sarah K. Buddenborg (811846)
Coen M. Adema (8876)
John T. Sullivan (290436)
Eric S. Loker (44887)

October 2015

<p>Note: Genes described in the table were found to be expressed differentially in at least one conc...

List of differentially expressed genes with fold change >3 selected for Case Study II.

Rajesh Chowdhary (67745)
Sin Lam Tan (16634)
Jinfeng Zhang (22473)
Shreyas Karnik (172689)
Vladimir B. Bajic (8687)
Jun S. Liu (15013)

April 2012

<p>List of differentially expressed genes with fold change >3 selected for Case Study II.</p

List of genes with differential expression in quiescent vs. proliferative HsFb.

Bo-Rui Chen (298785)
Huei-Hsuan Cheng (298786)
Wei-Chung Lin (298787)
Kai-Hsuan Wang (298788)
Jun-Yang Liou (154997)
Pei-Feng Chen (298789)
Kenneth K. Wu (154996)

February 2013

<p>List of genes with differential expression in quiescent vs. proliferative HsFb.</p

Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Arctic Centre, Univ. of Groningen
Wellcome Sanger Institute
Institute of Epidemiology 2
Technical University of Munich
University Medical Center Groningen
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell type

Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Arctic Centre, Univ. of Groningen
Wellcome Sanger Institute
Technical University of Munich
Institute of Epidemiology 2
University Medical Center Groningen
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell type

Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Arctic Centre, Univ. of Groningen
Wellcome Sanger Institute
Technical University of Munich
Institute of Epidemiology 2
University Medical Center Groningen
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell type

Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Arctic Centre, Univ. of Groningen
Wellcome Sanger Institute
Institute of Epidemiology 2
Technical University of Munich
University Medical Center Groningen
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell type

Table with the expressed genes that represents several statistical values of these genes.

Daniel Castillo (2608138)
Juan Manuel Galvez (6325697)
Luis J. Herrera (5082503)
Fernando Rojas (6325700)
Olga Valenzuela (5211047)
Octavio Caba (811156)
Jose Prados (778445)
Ignacio Rojas (5059148)

February 2019

Table with the expressed genes that represents several statistical values of these genes.</p

Supplementary Table 3a

Rintu Kutum (4494886)
Govind K Makharia (5440547)

June 2018

<p>Gene ontology enrichment results for differentially expressed genes among FDR, CeD and Control</p

Differentially expressed gene lists - unfiltered

John E. Collins (207876)
Richard J. White (35897)
Nicole Staudt (60273)
Ian M. Sealy (3719416)
Ian Packham (5473280)
Neha Wali (2205688)
Catherine Tudor (5473265)
Cecilia Mazzeo (5473283)
Angela Green (250894)
Emma Siragher (5473271)
Edward Ryder (145998)
Jacqueline K. White (119191)
Irene Papatheodoru (5473268)
Amy Tang (4337950)
Anja Füllgrabe (3719422)
Konstantinos Billis (650319)
Stefan H. Geyer (6306488)
Wolfgang J. Weninger (5516939)
Antonella Galli (250780)
Myriam Hemberger (93502)
Derek L. Stemple (595950)
Elizabeth Robertson (450547)
James C. Smith (68336)
Timothy Mohun (2940327)
David J. Adams (119198)
Elisabeth M. Busch-Nentwich (3719419)

March 2019

Files of differentially expressed genes (using DESeq2) from different mutant lines.see the README fo...

Number of significant differentially expressed genes within each comparative microarray group (filtered for fold change > 2 and p-value < 0.05).

N. Jumper (3812692)
T. Hodgkinson (3812695)
R. Paus (3812698)
A. Bayat (3812689)

March 2017

<p>Number of significant differentially expressed genes within each comparative microarray group (fi...

List of differentially expressed genes and uncharacterized transcripts (±2 fold change, q<0.05).

Jasmin H. Bavarva (422981)
Hongseok Tae (35265)
Robert E. Settlage (422982)
Harold R. Garner (6157)

June 2013

<p>List of differentially expressed genes and uncharacterized transcripts (±2 fold change, q<0.05).<...

Table containing differential expressed genes (result of edgeR)

Patel, Alok
Dettleff, Phillip
Hernández, Eric
Martinez, Victor

August 2015

This table contains data of list of genes that were < 0.01 FDR value and differed in their expressio...

Table containing differential expressed genes (result of edgeR)

Alok Patel (1408258)
Phillip Dettleff (3362153)
Eric Hernández (3362150)
Victor Martinez (2539555)

November 2016

This table contains data of list of genes that were < 0.01 FDR value and differed in their expressio...

Retrieved differentially expressed genes in CF (adapted from [31]).

Pascal Trouvé (317768)
Emmanuelle Génin (91542)
Claude Férec (204332)

March 2017

<p>The lower part of the table shows genes shared between two or more studies when all six studies a...

List of differentially expressed transcripts that have putative homologs in GenBank.

Si-Ming Zhang (811845)
Sarah K. Buddenborg (811846)
Coen M. Adema (8876)
John T. Sullivan (290436)
Eric S. Loker (44887)

October 2015

<p>Note: Genes described in the table were found to be expressed differentially in at least one conc...

List of differentially expressed genes with fold change >3 selected for Case Study II.

Rajesh Chowdhary (67745)
Sin Lam Tan (16634)
Jinfeng Zhang (22473)
Shreyas Karnik (172689)
Vladimir B. Bajic (8687)
Jun S. Liu (15013)

April 2012

<p>List of differentially expressed genes with fold change >3 selected for Case Study II.</p

List of genes with differential expression in quiescent vs. proliferative HsFb.

Bo-Rui Chen (298785)
Huei-Hsuan Cheng (298786)
Wei-Chung Lin (298787)
Kai-Hsuan Wang (298788)
Jun-Yang Liou (154997)
Pei-Feng Chen (298789)
Kenneth K. Wu (154996)

February 2013

<p>List of genes with differential expression in quiescent vs. proliferative HsFb.</p

Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Arctic Centre, Univ. of Groningen
Wellcome Sanger Institute
Institute of Epidemiology 2
Technical University of Munich
University Medical Center Groningen
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell type

Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Arctic Centre, Univ. of Groningen
Wellcome Sanger Institute
Technical University of Munich
Institute of Epidemiology 2
University Medical Center Groningen
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell type

Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Arctic Centre, Univ. of Groningen
Wellcome Sanger Institute
Technical University of Munich
Institute of Epidemiology 2
University Medical Center Groningen
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell type

Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Arctic Centre, Univ. of Groningen
Wellcome Sanger Institute
Institute of Epidemiology 2
Technical University of Munich
University Medical Center Groningen
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell type

Table with the expressed genes that represents several statistical values of these genes.

Daniel Castillo (2608138)
Juan Manuel Galvez (6325697)
Luis J. Herrera (5082503)
Fernando Rojas (6325700)
Olga Valenzuela (5211047)
Octavio Caba (811156)
Jose Prados (778445)
Ignacio Rojas (5059148)

February 2019

Table with the expressed genes that represents several statistical values of these genes.</p

Supplementary Table 3a

Rintu Kutum (4494886)
Govind K Makharia (5440547)

June 2018

<p>Gene ontology enrichment results for differentially expressed genes among FDR, CeD and Control</p

Differentially expressed gene lists - unfiltered

John E. Collins (207876)
Richard J. White (35897)
Nicole Staudt (60273)
Ian M. Sealy (3719416)
Ian Packham (5473280)
Neha Wali (2205688)
Catherine Tudor (5473265)
Cecilia Mazzeo (5473283)
Angela Green (250894)
Emma Siragher (5473271)
Edward Ryder (145998)
Jacqueline K. White (119191)
Irene Papatheodoru (5473268)
Amy Tang (4337950)
Anja Füllgrabe (3719422)
Konstantinos Billis (650319)
Stefan H. Geyer (6306488)
Wolfgang J. Weninger (5516939)
Antonella Galli (250780)
Myriam Hemberger (93502)
Derek L. Stemple (595950)
Elizabeth Robertson (450547)
James C. Smith (68336)
Timothy Mohun (2940327)
David J. Adams (119198)
Elisabeth M. Busch-Nentwich (3719419)

March 2019

Files of differentially expressed genes (using DESeq2) from different mutant lines.see the README fo...

Number of significant differentially expressed genes within each comparative microarray group (filtered for fold change > 2 and p-value < 0.05).

N. Jumper (3812692)
T. Hodgkinson (3812695)
R. Paus (3812698)
A. Bayat (3812689)

March 2017

<p>Number of significant differentially expressed genes within each comparative microarray group (fi...

List of differentially expressed genes and uncharacterized transcripts (±2 fold change, q<0.05).

Jasmin H. Bavarva (422981)
Hongseok Tae (35265)
Robert E. Settlage (422982)
Harold R. Garner (6157)

June 2013

<p>List of differentially expressed genes and uncharacterized transcripts (±2 fold change, q<0.05).<...