Additional file 9: Table S5. of The Drosophila transcriptional network is structured by microbiota

Additional file 4: of A modular analysis of microglia gene expression, insights into the aged phenotype

Christine Cho (1749574)
Sagar Damle (4766640)
Edward Wancewicz (6414020)
Swagatam Mukhopadhyay (434948)
Christopher Hart (6414023)
Curt Mazur (185224)
Eric Swayze (6414026)
Fredrik Kamme (6414029)

March 2019

Table S4 Gene Ontology (GO) terms associated with each module. Columns show the GO term and correspo...

Identification of functional elements and regulatory circuits by Drosophila modENCODE

Roy, Sushmita
Ernst, Jason
Kharchenko, Peter V.
Kheradpour, Pouya
Negre, Nicolas
Eaton, Matthew L.
Landolin, Jane M.
Bristow, Christopher A.
Ma, Lijia
Lin, Michael F.
Washietl, Stefan
Arshinoff, Bradley I.
Ay, Ferhat
Meyer, Patrick E.
Robine, Nicolas
Washington, Nicole L.
Stefano, Luisa Di
Berezikov, Eugene
Brown, Christopher D.
Candeias, Rogerio
Carlson, Joseph W.
Carr, Adrian
Jungreis, Irwin
Marbach, Daniel
Sealfon, Rachel
Tolstorukov, Michael Y.
Will, Sebastian
Alekseyenko, Artyom A.
Artieri, Carlo
Booth, Benjamin W.
Brooks, Angela N.
Dai, Qi
Davis, Carrie A.
Duff, Michael O.
Feng, Xin
Gorchakov, Andrey A.
Gu, Tingting
Henikoff, Jorja G.
Kapranov, Philipp
Li, Renhua
MacAlpine, Heather K.
Malone, John
Minoda, Aki
Nordman, Jared
Okamura, Katsutomo
Perry, Marc
Powell, Sara K.
Riddle, Nicole C.
Sakai, Akiko
Samsonova, Anastasia
Sandler, Jeremy E.
Schwartz, Yuri B.
Sher, Noa
Spokony, Rebecca
Sturgill, David
van Baren, Marijke
Wan, Kenneth H.
Yang, Li
Yu, Charles
Feingold, Elise
Good, Peter
Guyer, Mark
Lowdon, Rebecca
Ahmad, Kami
Andrews, Justen
Berger, Bonnie
Brenner, Steven E.
Brent, Michael R.
Cherbas, Lucy
Elgin, Sarah C. R.
Gingeras, Thomas R.
Grossman, Robert
Hoskins, Roger A.
Kaufman, Thomas C.
Kent, William
Kuroda, Mitzi I.
Orr-Weaver, Terry
Perrimon, Norbert
Pirrotta, Vincenzo
Posakony, James W.
Ren, Bing
Russell, Steven
Cherbas, Peter
Graveley, Brenton R.
Lewis, Suzanna
Micklem, Gos
Oliver, Brian
Park, Peter J.
Celniker, Susan E.
Henikoff, Steven
Karpen, Gary H.
Lai, Eric C.
MacAlpine, David M.
Stein, Lincoln D.
White, Kevin P.
Kellis, Manolis

December 2010

To gain insight into how genomic information is translated into cellular and developmental programs,...

Additional file 6 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

Castro-Melchor, Marlene
Charaniya, Salim
Karypis, George
Takano, Eriko
Hu, Wei-Shou
Host-Microbe Interactions

April 2021

Additional file 6: Enriched networks. Worksheet 1 contains the list of network modules enriched acco...

Additional file 5: Table S3. of The Drosophila transcriptional network is structured by microbiota

Adam Dobson (774336)
John Chaston (3579071)
Angela Douglas (3545993)

November 2016

Gene membership of transcriptional modules. The table shows gene identifiers and names in FlyBase fo...

Additional file 6: Table S4. of The Drosophila transcriptional network is structured by microbiota

Adam Dobson (774336)
John Chaston (3579071)
Angela Douglas (3545993)

November 2016

Frequency of data permutations with dispersion statistic greater than observed, within individual mo...

Additional file 13: Dataset S1. of The Drosophila transcriptional network is structured by microbiota

Adam Dobson (774336)
John Chaston (3579071)
Angela Douglas (3545993)

November 2016

Read counts per gene. Each column denotes a different sample. See Table S4 for line name information...

Drosophila microbiota impacts midgut genes expression.

Berra Erkosar Combe (551347)
Arnaud Defaye (551348)
Noémie Bozonnet (551349)
Denis Puthier (87106)
Julien Royet (201408)
François Leulier (369470)

April 2014

(A) A schematic representation of the experimental set-up used for transcriptome analysis; GF: Ge...

Additional file 4: of Analysis of Drosophila melanogaster testis transcriptome

Viktor Vedelek (2967072)
László Bodai (152655)
Gábor Grézal (5784083)
Bence Kovács (3256365)
Imre Boros (603616)
Barbara Laurinyecz (2967069)
Rita Sinka (2967066)

November 2018

Full network of the analysed FlyBase Gene Group data visualised by Cytoscape. Cytoscape session file...

Additional file 14: Dataset S2. of The Drosophila transcriptional network is structured by microbiota

Adam Dobson (774336)
John Chaston (3579071)
Angela Douglas (3545993)

November 2016

Variance-stabilized read counts. Dataset S1 with a variance-stabilising transformation applied using...

Additional file 17: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Charikleia Karageorgiou (6477824)
Víctor Gámez-Visairas (6477827)
Rosa Tarrío (347573)
Francisco Rodríguez-Trelles (347575)

March 2019

Figure S10. REVIGO summary scatterplot for 8 over-represented Cellular Component GO terms in CAFE-co...

Additional file 15: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Charikleia Karageorgiou (6477824)
Víctor Gámez-Visairas (6477827)
Rosa Tarrío (347573)
Francisco Rodríguez-Trelles (347575)

March 2019

Figure S8. REVIGO summary scatterplot for 51 over-represented Biological Process GO terms in CAFE-co...

Additional file 5: Figure S2. of RNA sequencing to characterize transcriptional changes of sexual maturation and mating in the female oriental fruit fly Bactrocera dorsalis

Weiwei Zheng (140828)
Deye Luo (3588170)
Fangyu Wu (3588167)
Jialu Wang (708905)
Hongyu Zhang (155876)

March 2016

Gene ontology (GO) analyses of transcriptome sequences predicted to participate in: (A) biological p...

Additional file 7 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

Castro-Melchor, Marlene
Charaniya, Salim
Karypis, George
Takano, Eriko
Hu, Wei-Shou
Host-Microbe Interactions

April 2021

Additional file 7: Details of the 20 network modules enriched in both a protein class and a GO term....

Additional file 12: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Charikleia Karageorgiou (6477824)
Víctor Gámez-Visairas (6477827)
Rosa Tarrío (347573)
Francisco Rodríguez-Trelles (347575)

March 2019

Figure S5. REVIGO summary scatterplot for 27 over-represented Biological Process GO terms in CAFE-ex...

Additional file 14: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Charikleia Karageorgiou (6477824)
Víctor Gámez-Visairas (6477827)
Rosa Tarrío (347573)
Francisco Rodríguez-Trelles (347575)

March 2019

Figure S7. REVIGO summary scatterplot for 9 over-represented Cellular Component GO terms in CAFE-exp...

Additional file 4: of A modular analysis of microglia gene expression, insights into the aged phenotype

Christine Cho (1749574)
Sagar Damle (4766640)
Edward Wancewicz (6414020)
Swagatam Mukhopadhyay (434948)
Christopher Hart (6414023)
Curt Mazur (185224)
Eric Swayze (6414026)
Fredrik Kamme (6414029)

March 2019

Table S4 Gene Ontology (GO) terms associated with each module. Columns show the GO term and correspo...

Identification of functional elements and regulatory circuits by Drosophila modENCODE

Roy, Sushmita
Ernst, Jason
Kharchenko, Peter V.
Kheradpour, Pouya
Negre, Nicolas
Eaton, Matthew L.
Landolin, Jane M.
Bristow, Christopher A.
Ma, Lijia
Lin, Michael F.
Washietl, Stefan
Arshinoff, Bradley I.
Ay, Ferhat
Meyer, Patrick E.
Robine, Nicolas
Washington, Nicole L.
Stefano, Luisa Di
Berezikov, Eugene
Brown, Christopher D.
Candeias, Rogerio
Carlson, Joseph W.
Carr, Adrian
Jungreis, Irwin
Marbach, Daniel
Sealfon, Rachel
Tolstorukov, Michael Y.
Will, Sebastian
Alekseyenko, Artyom A.
Artieri, Carlo
Booth, Benjamin W.
Brooks, Angela N.
Dai, Qi
Davis, Carrie A.
Duff, Michael O.
Feng, Xin
Gorchakov, Andrey A.
Gu, Tingting
Henikoff, Jorja G.
Kapranov, Philipp
Li, Renhua
MacAlpine, Heather K.
Malone, John
Minoda, Aki
Nordman, Jared
Okamura, Katsutomo
Perry, Marc
Powell, Sara K.
Riddle, Nicole C.
Sakai, Akiko
Samsonova, Anastasia
Sandler, Jeremy E.
Schwartz, Yuri B.
Sher, Noa
Spokony, Rebecca
Sturgill, David
van Baren, Marijke
Wan, Kenneth H.
Yang, Li
Yu, Charles
Feingold, Elise
Good, Peter
Guyer, Mark
Lowdon, Rebecca
Ahmad, Kami
Andrews, Justen
Berger, Bonnie
Brenner, Steven E.
Brent, Michael R.
Cherbas, Lucy
Elgin, Sarah C. R.
Gingeras, Thomas R.
Grossman, Robert
Hoskins, Roger A.
Kaufman, Thomas C.
Kent, William
Kuroda, Mitzi I.
Orr-Weaver, Terry
Perrimon, Norbert
Pirrotta, Vincenzo
Posakony, James W.
Ren, Bing
Russell, Steven
Cherbas, Peter
Graveley, Brenton R.
Lewis, Suzanna
Micklem, Gos
Oliver, Brian
Park, Peter J.
Celniker, Susan E.
Henikoff, Steven
Karpen, Gary H.
Lai, Eric C.
MacAlpine, David M.
Stein, Lincoln D.
White, Kevin P.
Kellis, Manolis

December 2010

To gain insight into how genomic information is translated into cellular and developmental programs,...

Additional file 6 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

Castro-Melchor, Marlene
Charaniya, Salim
Karypis, George
Takano, Eriko
Hu, Wei-Shou
Host-Microbe Interactions

April 2021

Additional file 6: Enriched networks. Worksheet 1 contains the list of network modules enriched acco...

Additional file 5: Table S3. of The Drosophila transcriptional network is structured by microbiota

Adam Dobson (774336)
John Chaston (3579071)
Angela Douglas (3545993)

November 2016

Gene membership of transcriptional modules. The table shows gene identifiers and names in FlyBase fo...

Additional file 6: Table S4. of The Drosophila transcriptional network is structured by microbiota

Adam Dobson (774336)
John Chaston (3579071)
Angela Douglas (3545993)

November 2016

Frequency of data permutations with dispersion statistic greater than observed, within individual mo...

Additional file 13: Dataset S1. of The Drosophila transcriptional network is structured by microbiota

Adam Dobson (774336)
John Chaston (3579071)
Angela Douglas (3545993)

November 2016

Read counts per gene. Each column denotes a different sample. See Table S4 for line name information...

Drosophila microbiota impacts midgut genes expression.

Berra Erkosar Combe (551347)
Arnaud Defaye (551348)
Noémie Bozonnet (551349)
Denis Puthier (87106)
Julien Royet (201408)
François Leulier (369470)

April 2014

(A) A schematic representation of the experimental set-up used for transcriptome analysis; GF: Ge...

Additional file 4: of Analysis of Drosophila melanogaster testis transcriptome

Viktor Vedelek (2967072)
László Bodai (152655)
Gábor Grézal (5784083)
Bence Kovács (3256365)
Imre Boros (603616)
Barbara Laurinyecz (2967069)
Rita Sinka (2967066)

November 2018

Full network of the analysed FlyBase Gene Group data visualised by Cytoscape. Cytoscape session file...

Additional file 14: Dataset S2. of The Drosophila transcriptional network is structured by microbiota

Adam Dobson (774336)
John Chaston (3579071)
Angela Douglas (3545993)

November 2016

Variance-stabilized read counts. Dataset S1 with a variance-stabilising transformation applied using...

Additional file 17: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Charikleia Karageorgiou (6477824)
Víctor Gámez-Visairas (6477827)
Rosa Tarrío (347573)
Francisco Rodríguez-Trelles (347575)

March 2019

Figure S10. REVIGO summary scatterplot for 8 over-represented Cellular Component GO terms in CAFE-co...

Additional file 15: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Charikleia Karageorgiou (6477824)
Víctor Gámez-Visairas (6477827)
Rosa Tarrío (347573)
Francisco Rodríguez-Trelles (347575)

March 2019

Figure S8. REVIGO summary scatterplot for 51 over-represented Biological Process GO terms in CAFE-co...

Additional file 5: Figure S2. of RNA sequencing to characterize transcriptional changes of sexual maturation and mating in the female oriental fruit fly Bactrocera dorsalis

Weiwei Zheng (140828)
Deye Luo (3588170)
Fangyu Wu (3588167)
Jialu Wang (708905)
Hongyu Zhang (155876)

March 2016

Gene ontology (GO) analyses of transcriptome sequences predicted to participate in: (A) biological p...

Additional file 7 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

Castro-Melchor, Marlene
Charaniya, Salim
Karypis, George
Takano, Eriko
Hu, Wei-Shou
Host-Microbe Interactions

April 2021

Additional file 7: Details of the 20 network modules enriched in both a protein class and a GO term....

Additional file 12: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Charikleia Karageorgiou (6477824)
Víctor Gámez-Visairas (6477827)
Rosa Tarrío (347573)
Francisco Rodríguez-Trelles (347575)

March 2019

Figure S5. REVIGO summary scatterplot for 27 over-represented Biological Process GO terms in CAFE-ex...

Additional file 14: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Charikleia Karageorgiou (6477824)
Víctor Gámez-Visairas (6477827)
Rosa Tarrío (347573)
Francisco Rodríguez-Trelles (347575)

March 2019

Figure S7. REVIGO summary scatterplot for 9 over-represented Cellular Component GO terms in CAFE-exp...

Additional file 4: of A modular analysis of microglia gene expression, insights into the aged phenotype

Christine Cho (1749574)
Sagar Damle (4766640)
Edward Wancewicz (6414020)
Swagatam Mukhopadhyay (434948)
Christopher Hart (6414023)
Curt Mazur (185224)
Eric Swayze (6414026)
Fredrik Kamme (6414029)

March 2019

Table S4 Gene Ontology (GO) terms associated with each module. Columns show the GO term and correspo...

Identification of functional elements and regulatory circuits by Drosophila modENCODE

Roy, Sushmita
Ernst, Jason
Kharchenko, Peter V.
Kheradpour, Pouya
Negre, Nicolas
Eaton, Matthew L.
Landolin, Jane M.
Bristow, Christopher A.
Ma, Lijia
Lin, Michael F.
Washietl, Stefan
Arshinoff, Bradley I.
Ay, Ferhat
Meyer, Patrick E.
Robine, Nicolas
Washington, Nicole L.
Stefano, Luisa Di
Berezikov, Eugene
Brown, Christopher D.
Candeias, Rogerio
Carlson, Joseph W.
Carr, Adrian
Jungreis, Irwin
Marbach, Daniel
Sealfon, Rachel
Tolstorukov, Michael Y.
Will, Sebastian
Alekseyenko, Artyom A.
Artieri, Carlo
Booth, Benjamin W.
Brooks, Angela N.
Dai, Qi
Davis, Carrie A.
Duff, Michael O.
Feng, Xin
Gorchakov, Andrey A.
Gu, Tingting
Henikoff, Jorja G.
Kapranov, Philipp
Li, Renhua
MacAlpine, Heather K.
Malone, John
Minoda, Aki
Nordman, Jared
Okamura, Katsutomo
Perry, Marc
Powell, Sara K.
Riddle, Nicole C.
Sakai, Akiko
Samsonova, Anastasia
Sandler, Jeremy E.
Schwartz, Yuri B.
Sher, Noa
Spokony, Rebecca
Sturgill, David
van Baren, Marijke
Wan, Kenneth H.
Yang, Li
Yu, Charles
Feingold, Elise
Good, Peter
Guyer, Mark
Lowdon, Rebecca
Ahmad, Kami
Andrews, Justen
Berger, Bonnie
Brenner, Steven E.
Brent, Michael R.
Cherbas, Lucy
Elgin, Sarah C. R.
Gingeras, Thomas R.
Grossman, Robert
Hoskins, Roger A.
Kaufman, Thomas C.
Kent, William
Kuroda, Mitzi I.
Orr-Weaver, Terry
Perrimon, Norbert
Pirrotta, Vincenzo
Posakony, James W.
Ren, Bing
Russell, Steven
Cherbas, Peter
Graveley, Brenton R.
Lewis, Suzanna
Micklem, Gos
Oliver, Brian
Park, Peter J.
Celniker, Susan E.
Henikoff, Steven
Karpen, Gary H.
Lai, Eric C.
MacAlpine, David M.
Stein, Lincoln D.
White, Kevin P.
Kellis, Manolis

December 2010

To gain insight into how genomic information is translated into cellular and developmental programs,...

Additional file 6 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

Castro-Melchor, Marlene
Charaniya, Salim
Karypis, George
Takano, Eriko
Hu, Wei-Shou
Host-Microbe Interactions

April 2021

Additional file 6: Enriched networks. Worksheet 1 contains the list of network modules enriched acco...

Additional file 9: Table S5. of The Drosophila transcriptional network is structured by microbiota

Abstract

Extracted data

Additional file 9: Table S5. of The Drosophila transcriptional network is structured by microbiota

Abstract

Extracted data

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