Additional file 2: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Additional file 3: Table S2. of Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291

Catherine Isom (3453839)
Smita Menon (2097619)
Leonard Thomas (1929799)
Ann West (3453833)
George Richter-Addo (3453842)
Elizabeth Karr (3453836)

October 2016

List of GLAM2Scan [24] results for scan of the Clostridium difficile R20291 genome for cdPadR1 motif...

Additional file 2: of G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs

Marco Di Salvo (4831365)
Eva Pinatel (4431565)
Adelfia TalĂ (4831368)
Marco Fondi (66036)
Clelia Peano (67208)
Pietro Alifano (70214)

February 2018

Coordinates of the validated promoters identified by G4PromFinder in S. coelicolor A3(2). (XLSX 100 ...

Additional file 2: of Structure, clustering and functional insights of repeats configurations in the upstream promoter region of the human coding genes

Fabian Tobar-Tosse (6075554)
Patricia VelĂŠz (6075557)
Eliana Ocampo-Toro (6075560)
Pedro Moreno (2274892)

December 2018

List of Repeat configurations in the upstream promoter region of the human genes, full list. (XLSX 5...

Additional file 1: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Table S1. TATA box motif prediction. Pval cutoff 10exp-2; origin = START; only direct strand results...

Additional file 3: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Table S3. DPE motif prediction. Pval cutoff 10exp-2; origin = START; only direct strand results are ...

Additional file 6: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Figure S2. Luciferase-promoter assay in S2R+ cells. Individual promoter-luciferase assay results in ...

Additional file 8: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Figure S4. Luciferase-promoter assay in bacteria (DH5alpha cells). Individual promoter-luciferase as...

Additional file 5: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Figure S1. Luciferase-promoter assay in HeLa cells. Individual promoter-luciferase assay results in ...

Additional file 7: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Figure S3. Luciferase-promoter assay in S. cerevisiae cells (BMA64-1A). Individual promoter-lucifera...

Additional file 3: of Selective translational usage of TSS and core promoters revealed by translatome sequencing

Hua Li (46469)
Ling Bai (82594)
Hongmei Li (51944)
Xinhui Li (349485)
Yani Kang (698978)
Ningbo Zhang (591333)
Jielin Sun (123338)
Zhifeng Shao (698979)

April 2019

Table S1. TCs with changed 5’ end distributions between translatome and transcriptome. “Chr” stands ...

Additional file 9: of Selective translational usage of TSS and core promoters revealed by translatome sequencing

Hua Li (46469)
Ling Bai (82594)
Hongmei Li (51944)
Xinhui Li (349485)
Yani Kang (698978)
Ningbo Zhang (591333)
Jielin Sun (123338)
Zhifeng Shao (698979)

April 2019

Table S6. Differential usage of core promoters from the same gene by polysome. Under each gene name,...

Additional file 4: Table S3. of Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291

Catherine Isom (3453839)
Smita Menon (2097619)
Leonard Thomas (1929799)
Ann West (3453833)
George Richter-Addo (3453842)
Elizabeth Karr (3453836)

October 2016

List of GLAM2Scan [24] results for scan of the Clostridium difficile R20291 genome for cdPadR1 motif...

Additional file 2: Table S2. of The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts

Adam Kolondra (215821)
Karolina Labedzka-Dmoch (3474398)
Joanna Wenda (3474392)
Katarzyna Drzewicka (3474395)
Pawel Golik (3474401)

October 2015

Promoters and promoter-like sequences in C. albicans mtDNA. Promoters of the primary transcription u...

Additional file 2: of Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines

Jiayue-Clara Jiang (6642887)
Kyle Upton (3587213)

April 2019

CAGE clusters and genes mapped to putative TE-derived promoters: contains the list of CAGE clusters ...

Additional file 2: of The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype

Francois-Xavier Dieudonné (3519875)
Patrick O’Connor (3519866)
Pascale Gubler-Jaquier (3519860)
Haleh Yasrebi (257934)
Beatrice Conne (3519872)
Sergey Nikolaev (274006)
Stylianos Antonarakis (3519869)
Pavel Baranov (3519863)
Joseph Curran (600788)

November 2015

A: Differential gene expression analysis with polysomal RNAseq. Cuffdiff summary including fold chan...

Additional file 3: Table S2. of Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291

Catherine Isom (3453839)
Smita Menon (2097619)
Leonard Thomas (1929799)
Ann West (3453833)
George Richter-Addo (3453842)
Elizabeth Karr (3453836)

October 2016

List of GLAM2Scan [24] results for scan of the Clostridium difficile R20291 genome for cdPadR1 motif...

Additional file 2: of G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs

Marco Di Salvo (4831365)
Eva Pinatel (4431565)
Adelfia TalĂ (4831368)
Marco Fondi (66036)
Clelia Peano (67208)
Pietro Alifano (70214)

February 2018

Coordinates of the validated promoters identified by G4PromFinder in S. coelicolor A3(2). (XLSX 100 ...

Additional file 2: of Structure, clustering and functional insights of repeats configurations in the upstream promoter region of the human coding genes

Fabian Tobar-Tosse (6075554)
Patricia VelĂŠz (6075557)
Eliana Ocampo-Toro (6075560)
Pedro Moreno (2274892)

December 2018

List of Repeat configurations in the upstream promoter region of the human genes, full list. (XLSX 5...

Additional file 1: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Table S1. TATA box motif prediction. Pval cutoff 10exp-2; origin = START; only direct strand results...

Additional file 3: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Table S3. DPE motif prediction. Pval cutoff 10exp-2; origin = START; only direct strand results are ...

Additional file 6: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Figure S2. Luciferase-promoter assay in S2R+ cells. Individual promoter-luciferase assay results in ...

Additional file 8: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Figure S4. Luciferase-promoter assay in bacteria (DH5alpha cells). Individual promoter-luciferase as...

Additional file 5: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Figure S1. Luciferase-promoter assay in HeLa cells. Individual promoter-luciferase assay results in ...

Additional file 7: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Figure S3. Luciferase-promoter assay in S. cerevisiae cells (BMA64-1A). Individual promoter-lucifera...

Additional file 3: of Selective translational usage of TSS and core promoters revealed by translatome sequencing

Hua Li (46469)
Ling Bai (82594)
Hongmei Li (51944)
Xinhui Li (349485)
Yani Kang (698978)
Ningbo Zhang (591333)
Jielin Sun (123338)
Zhifeng Shao (698979)

April 2019

Table S1. TCs with changed 5’ end distributions between translatome and transcriptome. “Chr” stands ...

Additional file 9: of Selective translational usage of TSS and core promoters revealed by translatome sequencing

Hua Li (46469)
Ling Bai (82594)
Hongmei Li (51944)
Xinhui Li (349485)
Yani Kang (698978)
Ningbo Zhang (591333)
Jielin Sun (123338)
Zhifeng Shao (698979)

April 2019

Table S6. Differential usage of core promoters from the same gene by polysome. Under each gene name,...

Additional file 4: Table S3. of Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291

Catherine Isom (3453839)
Smita Menon (2097619)
Leonard Thomas (1929799)
Ann West (3453833)
George Richter-Addo (3453842)
Elizabeth Karr (3453836)

October 2016

List of GLAM2Scan [24] results for scan of the Clostridium difficile R20291 genome for cdPadR1 motif...

Additional file 2: Table S2. of The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts

Adam Kolondra (215821)
Karolina Labedzka-Dmoch (3474398)
Joanna Wenda (3474392)
Katarzyna Drzewicka (3474395)
Pawel Golik (3474401)

October 2015

Promoters and promoter-like sequences in C. albicans mtDNA. Promoters of the primary transcription u...

Additional file 2: of Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines

Jiayue-Clara Jiang (6642887)
Kyle Upton (3587213)

April 2019

CAGE clusters and genes mapped to putative TE-derived promoters: contains the list of CAGE clusters ...

Additional file 2: of The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype

Francois-Xavier Dieudonné (3519875)
Patrick O’Connor (3519866)
Pascale Gubler-Jaquier (3519860)
Haleh Yasrebi (257934)
Beatrice Conne (3519872)
Sergey Nikolaev (274006)
Stylianos Antonarakis (3519869)
Pavel Baranov (3519863)
Joseph Curran (600788)

November 2015

A: Differential gene expression analysis with polysomal RNAseq. Cuffdiff summary including fold chan...

Additional file 3: Table S2. of Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291

Catherine Isom (3453839)
Smita Menon (2097619)
Leonard Thomas (1929799)
Ann West (3453833)
George Richter-Addo (3453842)
Elizabeth Karr (3453836)

October 2016

List of GLAM2Scan [24] results for scan of the Clostridium difficile R20291 genome for cdPadR1 motif...

Additional file 2: of G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs

Marco Di Salvo (4831365)
Eva Pinatel (4431565)
Adelfia TalĂ (4831368)
Marco Fondi (66036)
Clelia Peano (67208)
Pietro Alifano (70214)

February 2018

Coordinates of the validated promoters identified by G4PromFinder in S. coelicolor A3(2). (XLSX 100 ...

Additional file 2: of Structure, clustering and functional insights of repeats configurations in the upstream promoter region of the human coding genes

Fabian Tobar-Tosse (6075554)
Patricia VelĂŠz (6075557)
Eliana Ocampo-Toro (6075560)
Pedro Moreno (2274892)

December 2018

List of Repeat configurations in the upstream promoter region of the human genes, full list. (XLSX 5...

Additional file 2: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Abstract

Extracted data

Topics

Additional file 2: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Abstract

Extracted data

Topics

Related items

Related items