Additional file 3: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-JosĂŠ Mercat (3574301)
Denis Milan (45336)
Laurence Liaubet (90101)

Publication date

December 2015

DOI

10.6084/m9.figshare.c.3642623_d3.v1

Abstract

Differentially expressed genes on autosomes. Only probes with an alignment on the porcine genome Sscrofa10.2 are reported with the corresponding annotation from Ensembl. The global and pairwise statistics are given for all the comparisons. DU: Duroc; LWF: Large White dam line; LWM: Large sire Male line; LR: Landrace; PI: PiĂŠtrain (XLSX 689Â kb

Extracted data

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Data Protection

Additional file 3: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-JosĂŠ Mercat (3574301)
Denis Milan (45336)
Laurence Liaubet (90101)

Open link

Publication date

December 2015

DOI

10.6084/m9.figshare.c.3642623_d3.v1

Abstract

Extracted data

Deborah Velez-Irizarry (6173753)
Sebastian Casiro (6173756)
Kaitlyn Daza (6173759)
Ronald Bates (6173762)
Nancy Raney (6173765)
Juan Steibel (6173768)
Catherine Ernst (5766908)

January 2019

Table S1. Expression quantitative trait loci (eQTL) mapped for longissimus dorsi muscle transcripts ...

Table_3_Comparison of differentially expressed genes in longissimus dorsi muscle of Diannan small ears, Wujin and landrace pigs using RNA-seq.XLSX

Qiuyan Li (526038)
Meilin Hao (17737449)
Junhong Zhu (13957638)
Lanlan Yi (13957635)
Wenjie Cheng (519724)
Yuxiao Xie (11532106)
Sumei Zhao (4163986)

January 2024

IntroductionPig growth is an important economic trait that involves the co-regulation of multiple ge...

Additional file 6: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S5. Correlations between the expression of genes regulated by cis-eQTL and the variation of ph...

Additional file 1: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-José Mercat (211636)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

1,859 genes were identified to be differentially expressed between five breeds according to statisti...

Additional file 5: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-JosĂŠ Mercat (3574301)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

228 spots (171 unique genes) allow the discrimination between the five lines. These genes were ident...

Additional file 2: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-JosĂŠ Mercat (3574301)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

Annotation of the regulated genes. This list of probes corresponds to the differential probes from t...

Additional file 6: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-JosĂŠ Mercat (3574301)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

EASE systematic functional annotation for the 683 unique differentially expressed genes. Detailed fu...

Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

San Cristobal, Magali
Rohart, Florian
Lascor, Christine
Bouffaud, Marcel
Trouilh, Lidwine
Martin, Pascal G.P.
Lippi, Yannick
Tribout, Thierry
Faraut, Thomas
Mercat, Marie-Jose
Milan, Denis
Liaubet, Laurence

January 2015

Notice a Reprendre pas de CLE UT au 17/12/2015Among transcriptomic studies, those comparing species ...

Additional file 4: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-José Mercat (211636)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

70 pathways enriched to explain the biologically diversity of five pig breeds. These pathways have b...

Additional file 3: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Figure S1. Genetic Power Calculator plots showing the power of the GWAS analysis (x-axis) for a popu...

Additional file 5: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S4. Genes located within QTL regions retrieved from the list of genes showing differential exp...

Additional file 1: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S1. List of genes differentially expressed between the gluteus medius and longissimus dorsi mu...

Additional file 10: of Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern

Xuelian Tao (18829)
Jianning Chen (3988352)
Yanzhi Jiang (785400)
Yingying Wei (823249)
Yan Chen (4308)
Huaming Xu (3988355)
Li Zhu (67404)
Guoqing Tang (785399)
Mingzhou Li (112100)
Anan Jiang (3988364)
Surong Shuai (112098)
Lin Bai (338207)
Haifeng Liu (117312)
Jideng Ma (112091)
Long Jin (112089)
Anxiang Wen (3988361)
Qin Wang (109812)
Guangxiang Zhu (3988358)
Meng Xie (501184)
Jiayun Wu (643690)
Tao He (23919)
Chunyu Huang (469230)
Xiang Gao (4077)
Xuewei Li (112102)

April 2017

data 8. Go analysis of breed-specific and -dynamic genes among three breeds. (XLS 2825Â kb

Additional file 2: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S2. Pathway Enrichment for genes differentially expressed between the gluteus medius and longi...

Additional file 3: of A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

Artur Gurgul (825970)
Igor Jasielczuk (825972)
Katarzyna Ropka-Molik (3908581)
Ewelina Semik-Gurgul (5880599)
Klaudia Pawlina-Tyszko (4814556)
Tomasz Szmatoła (4585621)
Magdalena Szyndler-Nędza (5880602)
Monika Bugno-Poniewierska (3908578)
Tadeusz Blicharski (3440384)
Karolina Szulc (5880605)
Ewa Skrzypczak (5880608)
Jędrzej Krupiński (5880611)

October 2018

Genes detected within the strongest diversifying selection signals detected in the studied pig breed...

Additional file 1: of Genetic control of longissimus dorsi muscle gene expression variation and joint analysis with phenotypic quantitative trait loci in pigs

Deborah Velez-Irizarry (6173753)
Sebastian Casiro (6173756)
Kaitlyn Daza (6173759)
Ronald Bates (6173762)
Nancy Raney (6173765)
Juan Steibel (6173768)
Catherine Ernst (5766908)

January 2019

Table S1. Expression quantitative trait loci (eQTL) mapped for longissimus dorsi muscle transcripts ...

Table_3_Comparison of differentially expressed genes in longissimus dorsi muscle of Diannan small ears, Wujin and landrace pigs using RNA-seq.XLSX

Qiuyan Li (526038)
Meilin Hao (17737449)
Junhong Zhu (13957638)
Lanlan Yi (13957635)
Wenjie Cheng (519724)
Yuxiao Xie (11532106)
Sumei Zhao (4163986)

January 2024

IntroductionPig growth is an important economic trait that involves the co-regulation of multiple ge...

Additional file 6: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S5. Correlations between the expression of genes regulated by cis-eQTL and the variation of ph...

Additional file 1: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-José Mercat (211636)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

1,859 genes were identified to be differentially expressed between five breeds according to statisti...

Additional file 5: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-JosĂŠ Mercat (3574301)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

228 spots (171 unique genes) allow the discrimination between the five lines. These genes were ident...

Additional file 2: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-JosĂŠ Mercat (3574301)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

Annotation of the regulated genes. This list of probes corresponds to the differential probes from t...

Additional file 6: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-JosĂŠ Mercat (3574301)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

EASE systematic functional annotation for the 683 unique differentially expressed genes. Detailed fu...

Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

San Cristobal, Magali
Rohart, Florian
Lascor, Christine
Bouffaud, Marcel
Trouilh, Lidwine
Martin, Pascal G.P.
Lippi, Yannick
Tribout, Thierry
Faraut, Thomas
Mercat, Marie-Jose
Milan, Denis
Liaubet, Laurence

January 2015

Notice a Reprendre pas de CLE UT au 17/12/2015Among transcriptomic studies, those comparing species ...

Additional file 4: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Magali SanCristobal (90102)
Florian Rohart (3574298)
Christine Lascor (3574286)
Marcel Bouffaud (211633)
Lidwine Trouilh (3432383)
Pascal G.P. Martin (3574292)
Yannick Lippi (3459740)
Thierry Tribout (3574295)
Thomas Faraut (3574289)
Marie-José Mercat (211636)
Denis Milan (45336)
Laurence Liaubet (90101)

December 2015

70 pathways enriched to explain the biologically diversity of five pig breeds. These pathways have b...

Additional file 3: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Figure S1. Genetic Power Calculator plots showing the power of the GWAS analysis (x-axis) for a popu...

Additional file 5: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S4. Genes located within QTL regions retrieved from the list of genes showing differential exp...

Additional file 1: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S1. List of genes differentially expressed between the gluteus medius and longissimus dorsi mu...

Xuelian Tao (18829)
Jianning Chen (3988352)
Yanzhi Jiang (785400)
Yingying Wei (823249)
Yan Chen (4308)
Huaming Xu (3988355)
Li Zhu (67404)
Guoqing Tang (785399)
Mingzhou Li (112100)
Anan Jiang (3988364)
Surong Shuai (112098)
Lin Bai (338207)
Haifeng Liu (117312)
Jideng Ma (112091)
Long Jin (112089)
Anxiang Wen (3988361)
Qin Wang (109812)
Guangxiang Zhu (3988358)
Meng Xie (501184)
Jiayun Wu (643690)
Tao He (23919)
Chunyu Huang (469230)
Xiang Gao (4077)
Xuewei Li (112102)

April 2017

data 8. Go analysis of breed-specific and -dynamic genes among three breeds. (XLS 2825Â kb

Additional file 2: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S2. Pathway Enrichment for genes differentially expressed between the gluteus medius and longi...

Additional file 3: of A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

Artur Gurgul (825970)
Igor Jasielczuk (825972)
Katarzyna Ropka-Molik (3908581)
Ewelina Semik-Gurgul (5880599)
Klaudia Pawlina-Tyszko (4814556)
Tomasz Szmatoła (4585621)
Magdalena Szyndler-Nędza (5880602)
Monika Bugno-Poniewierska (3908578)
Tadeusz Blicharski (3440384)
Karolina Szulc (5880605)
Ewa Skrzypczak (5880608)
Jędrzej Krupiński (5880611)

October 2018

Genes detected within the strongest diversifying selection signals detected in the studied pig breed...

Additional file 1: of Genetic control of longissimus dorsi muscle gene expression variation and joint analysis with phenotypic quantitative trait loci in pigs

Deborah Velez-Irizarry (6173753)
Sebastian Casiro (6173756)
Kaitlyn Daza (6173759)
Ronald Bates (6173762)
Nancy Raney (6173765)
Juan Steibel (6173768)
Catherine Ernst (5766908)

January 2019

Table S1. Expression quantitative trait loci (eQTL) mapped for longissimus dorsi muscle transcripts ...

Table_3_Comparison of differentially expressed genes in longissimus dorsi muscle of Diannan small ears, Wujin and landrace pigs using RNA-seq.XLSX

Qiuyan Li (526038)
Meilin Hao (17737449)
Junhong Zhu (13957638)
Lanlan Yi (13957635)
Wenjie Cheng (519724)
Yuxiao Xie (11532106)
Sumei Zhao (4163986)

January 2024

IntroductionPig growth is an important economic trait that involves the co-regulation of multiple ge...

Additional file 6: of Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles

Rayner González-Prendes (4349755)
Raquel Quintanilla (168993)
Emilio Mármol-Sánchez (4349752)
Ramona Pena (6423104)
Maria Ballester (103767)
Tainã Cardoso (3585575)
Arianna Manunza (383157)
Joaquim Casellas (94879)
Ángela Cánovas (3391583)
Isabel Díaz (2698609)
José Noguera (6423107)
Anna Castelló (277282)
Anna Mercadé (383164)
Marcel Amills (168991)

March 2019

Table S5. Correlations between the expression of genes regulated by cis-eQTL and the variation of ph...

Additional file 3: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Abstract

Extracted data

Additional file 3: of Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Abstract

Extracted data

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