Additional file 9: Table S4. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Additional file 9 of Insights into the architecture of human-induced polygenic selection in Duroc pigs

Zitao Chen (6433136)
Jinyan Teng (5705546)
Shuqi Diao (8666547)
Zhiting Xu (13835347)
Shaopan Ye (4987505)
Dingjie Qiu (13835350)
Zhe Zhang (81603)
Yuchun Pan (102909)
Jiaqi Li (220961)
Qin Zhang (58638)
Zhe Zhang (9711115)

September 2022

Additional file 9: Fig. S9. QTL enrichment results of the potential selection regions around rs34633...

Additional file 4: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Locations, gene identifiers, and tandem classifications for all discovered tandem NLRs in eight gras...

Additional file 1: of Homologous recombination occurs frequently at innate GT microsatellites in normal somatic and germ cells in vivo

Jianbo Zheng (502464)
Heng Li (6476)
Qi Zhang (28502)
Lei Sun (45752)
Xiangfang Liu (5212031)
Chen Luo (302288)

May 2018

Genome sequences of the paternal and maternal ntl promoter region containing the (GT)n motifs. Figur...

Additional file 8: Figure S5. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Masahiro Uesaka (3913591)
Kiyokazu Agata (30383)
Takao Oishi (586741)
Kinichi Nakashima (53665)
Takuya Imamura (3913594)

April 2017

The DNA motifs enriched at the immediately upstream regions of the TSS of pancRNA-partnered genes. T...

Additional file 11: Figure S7. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Masahiro Uesaka (3913591)
Kiyokazu Agata (30383)
Takao Oishi (586741)
Kinichi Nakashima (53665)
Takuya Imamura (3913594)

April 2017

Diversity of conserved pancRNA expression profile of the five tissues in the five species. Hierarchi...

Additional file 5: Figure S3. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Masahiro Uesaka (3913591)
Kiyokazu Agata (30383)
Takao Oishi (586741)
Kinichi Nakashima (53665)
Takuya Imamura (3913594)

April 2017

Histone modification across the regions around TSSs of each tissue-specific gene. RPM (Read count pe...

Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Uesaka, Masahiro
Agata, Kiyokazu
Oishi, Takao
Nakashima, Kinichi
Imamura, Takuya

April 2017

[Background]Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play extensi...

Additional file 3: of Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Jenny Chen (165315)
Alexander Shishkin (3095226)
Xiaopeng Zhu (16758)
Sabah Kadri (190360)
Itay Maza (3485990)
Mitchell Guttman (78794)
Jacob Hanna (23165)
Aviv Regev (147110)
Manuel Garber (3485987)

February 2016

Bed file of lncRNAs discovered from mouse (mm9), human (hg19), chimp/bonobo (panTro4), and rat (rn5)...

Additional file 4: of Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Jenny Chen (165315)
Alexander Shishkin (3095226)
Xiaopeng Zhu (16758)
Sabah Kadri (190360)
Itay Maza (3485990)
Mitchell Guttman (78794)
Jacob Hanna (23165)
Aviv Regev (147110)
Manuel Garber (3485987)

February 2016

Excel file of evolutionary metrics of all lncRNAs found to be conserved to the human/chimp/rat/mouse...

Additional file 2: Table S2. of Selection on different genes with equivalent functions: the convergence story told by Hox genes along the evolution of aquatic mammalian lineages

Mariana Nery (3429554)
Brunno Borges (3429551)
Aline Dragalzew (3429557)
Tiana Kohlsdorf (120086)

May 2016

Hox clusters size of those mammals with sequenced genomes included in our study. (DOCX 114 kb

Additional file 1: Figure S1. of Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals

Nathaniel Davies (3403241)
Peter Krusche (3403238)
Eran Tauber (514223)
Sascha Ott (192042)

October 2015

Association of CNEs with predicted nucleosome occupancy. Figure S2. Relationship of transcription fa...

Additional file 6: Figure S2. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

Estefania TarifeĂąo-Saldivia (3562199)
Arnaud Lavergne (3853447)
Alice Bernard (2552563)
Keerthana Padamata (3853444)
David Bergemann (3562187)
Marianne Voz (3562193)
Isabelle Manfroid (61481)
Bernard Peers (61486)

March 2017

Identification of genes with evolutionary conserved and enriched expression in pancreatic exocrine c...

Additional file 10: Figure S5. of New genes drive the evolution of gene interaction networks in the human and mouse genomes

Wenyu Zhang (227569)
Patrick Landback (200709)
Andrea Gschwend (3567077)
Bairong Shen (166580)
Manyuan Long (36802)

October 2015

Distribution of young genes (primate-specific genes) that originated from duplication-based and de n...

Additional file 4: Table S3. of Functionally conserved enhancers with divergent sequences in distant vertebrates

Song Yang (162335)
Nir Oksenberg (102535)
Sachiko Takayama (3555278)
Seok-Jin Heo (46279)
Alexander Poliakov (35431)
Nadav Ahituv (34361)
Inna Dubchak (3021)
Dario Boffelli (219692)

October 2015

Conserved transcription factor binding motifs in the five zebrafish/mouse syntenic enhancers. Identi...

Additional file 4: of Analysis of 5â gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals

Nathaniel Davies (3403241)
Peter Krusche (3403238)
Eran Tauber (514223)
Sascha Ott (192042)

October 2015

Standard Phylogibbs output for the RPLP2 CNE showing elicited motifs, their sequences, the organisms...

Additional file 9 of Insights into the architecture of human-induced polygenic selection in Duroc pigs

Zitao Chen (6433136)
Jinyan Teng (5705546)
Shuqi Diao (8666547)
Zhiting Xu (13835347)
Shaopan Ye (4987505)
Dingjie Qiu (13835350)
Zhe Zhang (81603)
Yuchun Pan (102909)
Jiaqi Li (220961)
Qin Zhang (58638)
Zhe Zhang (9711115)

September 2022

Additional file 9: Fig. S9. QTL enrichment results of the potential selection regions around rs34633...

Additional file 4: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Locations, gene identifiers, and tandem classifications for all discovered tandem NLRs in eight gras...

Additional file 1: of Homologous recombination occurs frequently at innate GT microsatellites in normal somatic and germ cells in vivo

Jianbo Zheng (502464)
Heng Li (6476)
Qi Zhang (28502)
Lei Sun (45752)
Xiangfang Liu (5212031)
Chen Luo (302288)

May 2018

Genome sequences of the paternal and maternal ntl promoter region containing the (GT)n motifs. Figur...

Additional file 8: Figure S5. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Masahiro Uesaka (3913591)
Kiyokazu Agata (30383)
Takao Oishi (586741)
Kinichi Nakashima (53665)
Takuya Imamura (3913594)

April 2017

The DNA motifs enriched at the immediately upstream regions of the TSS of pancRNA-partnered genes. T...

Additional file 11: Figure S7. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Masahiro Uesaka (3913591)
Kiyokazu Agata (30383)
Takao Oishi (586741)
Kinichi Nakashima (53665)
Takuya Imamura (3913594)

April 2017

Diversity of conserved pancRNA expression profile of the five tissues in the five species. Hierarchi...

Additional file 5: Figure S3. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Masahiro Uesaka (3913591)
Kiyokazu Agata (30383)
Takao Oishi (586741)
Kinichi Nakashima (53665)
Takuya Imamura (3913594)

April 2017

Histone modification across the regions around TSSs of each tissue-specific gene. RPM (Read count pe...

Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Uesaka, Masahiro
Agata, Kiyokazu
Oishi, Takao
Nakashima, Kinichi
Imamura, Takuya

April 2017

[Background]Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play extensi...

Additional file 3: of Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Jenny Chen (165315)
Alexander Shishkin (3095226)
Xiaopeng Zhu (16758)
Sabah Kadri (190360)
Itay Maza (3485990)
Mitchell Guttman (78794)
Jacob Hanna (23165)
Aviv Regev (147110)
Manuel Garber (3485987)

February 2016

Bed file of lncRNAs discovered from mouse (mm9), human (hg19), chimp/bonobo (panTro4), and rat (rn5)...

Additional file 4: of Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Jenny Chen (165315)
Alexander Shishkin (3095226)
Xiaopeng Zhu (16758)
Sabah Kadri (190360)
Itay Maza (3485990)
Mitchell Guttman (78794)
Jacob Hanna (23165)
Aviv Regev (147110)
Manuel Garber (3485987)

February 2016

Excel file of evolutionary metrics of all lncRNAs found to be conserved to the human/chimp/rat/mouse...

Additional file 2: Table S2. of Selection on different genes with equivalent functions: the convergence story told by Hox genes along the evolution of aquatic mammalian lineages

Mariana Nery (3429554)
Brunno Borges (3429551)
Aline Dragalzew (3429557)
Tiana Kohlsdorf (120086)

May 2016

Hox clusters size of those mammals with sequenced genomes included in our study. (DOCX 114 kb

Additional file 1: Figure S1. of Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals

Nathaniel Davies (3403241)
Peter Krusche (3403238)
Eran Tauber (514223)
Sascha Ott (192042)

October 2015

Association of CNEs with predicted nucleosome occupancy. Figure S2. Relationship of transcription fa...

Additional file 6: Figure S2. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

Estefania TarifeĂąo-Saldivia (3562199)
Arnaud Lavergne (3853447)
Alice Bernard (2552563)
Keerthana Padamata (3853444)
David Bergemann (3562187)
Marianne Voz (3562193)
Isabelle Manfroid (61481)
Bernard Peers (61486)

March 2017

Identification of genes with evolutionary conserved and enriched expression in pancreatic exocrine c...

Additional file 10: Figure S5. of New genes drive the evolution of gene interaction networks in the human and mouse genomes

Wenyu Zhang (227569)
Patrick Landback (200709)
Andrea Gschwend (3567077)
Bairong Shen (166580)
Manyuan Long (36802)

October 2015

Distribution of young genes (primate-specific genes) that originated from duplication-based and de n...

Additional file 4: Table S3. of Functionally conserved enhancers with divergent sequences in distant vertebrates

Song Yang (162335)
Nir Oksenberg (102535)
Sachiko Takayama (3555278)
Seok-Jin Heo (46279)
Alexander Poliakov (35431)
Nadav Ahituv (34361)
Inna Dubchak (3021)
Dario Boffelli (219692)

October 2015

Conserved transcription factor binding motifs in the five zebrafish/mouse syntenic enhancers. Identi...

Additional file 4: of Analysis of 5â gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals

Nathaniel Davies (3403241)
Peter Krusche (3403238)
Eran Tauber (514223)
Sascha Ott (192042)

October 2015

Standard Phylogibbs output for the RPLP2 CNE showing elicited motifs, their sequences, the organisms...

Additional file 9 of Insights into the architecture of human-induced polygenic selection in Duroc pigs

Zitao Chen (6433136)
Jinyan Teng (5705546)
Shuqi Diao (8666547)
Zhiting Xu (13835347)
Shaopan Ye (4987505)
Dingjie Qiu (13835350)
Zhe Zhang (81603)
Yuchun Pan (102909)
Jiaqi Li (220961)
Qin Zhang (58638)
Zhe Zhang (9711115)

September 2022

Additional file 9: Fig. S9. QTL enrichment results of the potential selection regions around rs34633...

Additional file 4: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Locations, gene identifiers, and tandem classifications for all discovered tandem NLRs in eight gras...

Additional file 1: of Homologous recombination occurs frequently at innate GT microsatellites in normal somatic and germ cells in vivo

Jianbo Zheng (502464)
Heng Li (6476)
Qi Zhang (28502)
Lei Sun (45752)
Xiangfang Liu (5212031)
Chen Luo (302288)

May 2018

Genome sequences of the paternal and maternal ntl promoter region containing the (GT)n motifs. Figur...

Additional file 9: Table S4. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Abstract

Extracted data

Additional file 9: Table S4. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

Abstract

Extracted data

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