Additional file 3: Table S1. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Additional file 3: Table S4. of IL-10 and integrin signaling pathways are associated with head and neck cancer progression

Sophia Bornstein (3515549)
Mark Schmidt (3172602)
Gabrielle Choonoo (3325773)
Trevor Levin (755264)
Joe Gray (94862)
Charles Thomas (1871524)
Melissa Wong (3032583)
Shannon McWeeney (39058)

January 2016

Pathways significantly enriched for differentially expressed (DE) genes between TCGA HNSCC progresso...

Additional file 3: Table S2. of A kinome siRNA screen identifies HGS as a potential target for liver cancers with oncogenic mutations in CTNNB1

Frédéric Canal (3179895)
Elodie Anthony (3461654)
Aurianne Lescure (310453)
Elaine Del Nery (310455)
Jacques Camonis (49694)
Franck Perez (259284)
Bruno Ragazzon (140444)
Christine Perret (365234)

December 2015

List of the 52 genes identified among the 687 tested genes in HT screening as important for the cell...

Additional file 6: of The molecular landscape of premenopausal breast cancer

Serena Liao (3582692)
Ryan Hartmaier (109111)
Kandace McGuire (3582695)
Shannon Puhalla (3582689)
Soumya Luthra (732484)
Uma Chandran (732485)
Tianzhou Ma (3582698)
Rohit Bhargava (562035)
Francesmary Modugno (757958)
Nancy Davidson (3512738)
Steve Benz (3582686)
Adrian Lee (3161067)
George Tseng (150934)
Steffi Oesterreich (109122)

August 2015

The Cancer Genome Atlas (TCGA) Ingenuity pathway analysis (IPA) upstream regulators. Table S1., Tabl...

Additional file 2: Figure S1. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
FranĂ§ois Bertucci (3586712)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Quality control studies of the shRNA screens. a Representative image showing the Pearson and Spearma...

Additional file 1: of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
Franรงois Bertucci (3586724)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Supplementary material and methods. Includes more detailed information about the methodology of the ...

Additional file 5: Figure S3. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
FranĂ§ois Bertucci (3586712)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Changes in the HDAC6 regulon network upon Ricolinostat treatment and HDAC6 score in primary breast c...

Additional file 6: Figure S4. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
Franรงois Bertucci (3586724)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Response to paclitaxel treatment in breast cancer cell line models. The bars indicates the normalize...

Additional file 4: Figure S2. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
FranĂ§ois Bertucci (3586712)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Inhibition of HDAC6 activity by small molecules in vitro and in vivo. The western blots show the acc...

Additional file 4: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan Bièche (3492)
Florence Lerebours (303656)
Céline Callens (424227)

August 2018

Figure S2. Comparison of biological pathway between IBC and non-IBC in four subgroups. (a) The perce...

Additional file 3: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan Bièche (3492)
Florence Lerebours (303656)
Céline Callens (424227)

August 2018

Figure S1. Comparison of somatic mutation frequency between IBC and non-IBC in four subgroups. (a) T...

Additional file 1: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan BiĂ¨che (5506235)
Florence Lerebours (303656)
CĂŠline Callens (5612045)

August 2018

Table S1. Pathological and clinical characteristics of non-IBC cohorts. (PDF 169 kb

Additional file 6: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

Anneleen Daemen (365394)
Gerard Manning (143099)

January 2018

Protein-coding genes associated with HER2 amplification. (A) List of 43 protein-coding genes with su...

Additional file 3: of Induction of cell cycle arrest and inflammatory genes by combined treatment with epigenetic, differentiating, and chemotherapeutic agents in triple-negative breast cancer

Vanessa Merino (6021092)
Soonweng Cho (6021095)
Nguyen Nguyen (566151)
Helen Sadik (6021098)
Athira Narayan (6021101)
Conover Talbot (6021104)
Leslie Cope (49815)
Xian Zhou (405014)
Zhe Zhang (81603)
BalĂĄzs GyĹrffy (4667755)
Saraswati Sukumar (11083)

November 2018

Table S1. ED genes in comparison to entinostat and doxorubicin treatments. (DOCX 41 kb

Additional file 2: Table S1. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response

Esther Lips (3581426)
Magali Michaut (76734)
Marlous Hoogstraat (630624)
Lennart Mulder (3581420)
Nicolle Besselink (630626)
Marco Koudijs (3581423)
Edwin Cuppen (9902)
Emile Voest (3581435)
Rene Bernards (3581432)
Petra Nederlof (3581429)
Jelle Wesseling (248405)
Sjoerd Rodenhuis (523940)
Lodewyk Wessels (66823)

October 2015

1977 Cancer Gene Panel. This file lists all 1,977 genes in the Cancer Gene Panel, used in this study...

Additional file 1: of HDAC is indispensable for IFN-γ-induced B7-H1 expression in gastric cancer

Rui Deng (157986)
Peng Zhang (2071)
Weizhen Liu (1418449)
Xiangyu Zeng (6075611)
Xianxiong Ma (4276441)
Liang Shi (8078)
Tao Wang (12008)
Yuping Yin (3617510)
Weilong Chang (838939)
Pei Zhang (232846)
Guobin Wang (322861)
Kaixiong Tao (281715)

December 2018

Figure S1. HDAC1–3 expression correlated B7-H1 expression in clinical gastric specimens. (A) B7-H1 a...

Additional file 3: Table S4. of IL-10 and integrin signaling pathways are associated with head and neck cancer progression

Sophia Bornstein (3515549)
Mark Schmidt (3172602)
Gabrielle Choonoo (3325773)
Trevor Levin (755264)
Joe Gray (94862)
Charles Thomas (1871524)
Melissa Wong (3032583)
Shannon McWeeney (39058)

January 2016

Pathways significantly enriched for differentially expressed (DE) genes between TCGA HNSCC progresso...

Additional file 3: Table S2. of A kinome siRNA screen identifies HGS as a potential target for liver cancers with oncogenic mutations in CTNNB1

Frédéric Canal (3179895)
Elodie Anthony (3461654)
Aurianne Lescure (310453)
Elaine Del Nery (310455)
Jacques Camonis (49694)
Franck Perez (259284)
Bruno Ragazzon (140444)
Christine Perret (365234)

December 2015

List of the 52 genes identified among the 687 tested genes in HT screening as important for the cell...

Additional file 6: of The molecular landscape of premenopausal breast cancer

Serena Liao (3582692)
Ryan Hartmaier (109111)
Kandace McGuire (3582695)
Shannon Puhalla (3582689)
Soumya Luthra (732484)
Uma Chandran (732485)
Tianzhou Ma (3582698)
Rohit Bhargava (562035)
Francesmary Modugno (757958)
Nancy Davidson (3512738)
Steve Benz (3582686)
Adrian Lee (3161067)
George Tseng (150934)
Steffi Oesterreich (109122)

August 2015

The Cancer Genome Atlas (TCGA) Ingenuity pathway analysis (IPA) upstream regulators. Table S1., Tabl...

Additional file 2: Figure S1. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
FranĂ§ois Bertucci (3586712)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Quality control studies of the shRNA screens. a Representative image showing the Pearson and Spearma...

Additional file 1: of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
Franรงois Bertucci (3586724)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Supplementary material and methods. Includes more detailed information about the methodology of the ...

Additional file 5: Figure S3. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
FranĂ§ois Bertucci (3586712)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Changes in the HDAC6 regulon network upon Ricolinostat treatment and HDAC6 score in primary breast c...

Additional file 6: Figure S4. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
Franรงois Bertucci (3586724)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Response to paclitaxel treatment in breast cancer cell line models. The bars indicates the normalize...

Additional file 4: Figure S2. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Preeti Putcha (370690)
Jiyang Yu (3586721)
Ruth Rodriguez-Barrueco (3586694)
Laura Saucedo-Cuevas (3586718)
Patricia Villagrasa (3586709)
Eva Murga-Penas (3586706)
Steven Quayle (3586700)
Min Yang (146229)
Veronica Castro (3586703)
David Llobet-Navas (3586715)
Daniel Birnbaum (63368)
Pascal Finetti (65359)
Wendy Woodward (3445817)
FranĂ§ois Bertucci (3586712)
Mary Alpaugh (3586697)
Andrea Califano (91999)
Jose Silva (269996)

December 2015

Inhibition of HDAC6 activity by small molecules in vitro and in vivo. The western blots show the acc...

Additional file 4: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan Bièche (3492)
Florence Lerebours (303656)
Céline Callens (424227)

August 2018

Figure S2. Comparison of biological pathway between IBC and non-IBC in four subgroups. (a) The perce...

Additional file 3: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan Bièche (3492)
Florence Lerebours (303656)
Céline Callens (424227)

August 2018

Figure S1. Comparison of somatic mutation frequency between IBC and non-IBC in four subgroups. (a) T...

Additional file 1: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan BiĂ¨che (5506235)
Florence Lerebours (303656)
CĂŠline Callens (5612045)

August 2018

Table S1. Pathological and clinical characteristics of non-IBC cohorts. (PDF 169 kb

Additional file 6: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

Anneleen Daemen (365394)
Gerard Manning (143099)

January 2018

Protein-coding genes associated with HER2 amplification. (A) List of 43 protein-coding genes with su...

Additional file 3: of Induction of cell cycle arrest and inflammatory genes by combined treatment with epigenetic, differentiating, and chemotherapeutic agents in triple-negative breast cancer

Vanessa Merino (6021092)
Soonweng Cho (6021095)
Nguyen Nguyen (566151)
Helen Sadik (6021098)
Athira Narayan (6021101)
Conover Talbot (6021104)
Leslie Cope (49815)
Xian Zhou (405014)
Zhe Zhang (81603)
BalĂĄzs GyĹrffy (4667755)
Saraswati Sukumar (11083)

November 2018

Table S1. ED genes in comparison to entinostat and doxorubicin treatments. (DOCX 41 kb

Additional file 2: Table S1. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response

Esther Lips (3581426)
Magali Michaut (76734)
Marlous Hoogstraat (630624)
Lennart Mulder (3581420)
Nicolle Besselink (630626)
Marco Koudijs (3581423)
Edwin Cuppen (9902)
Emile Voest (3581435)
Rene Bernards (3581432)
Petra Nederlof (3581429)
Jelle Wesseling (248405)
Sjoerd Rodenhuis (523940)
Lodewyk Wessels (66823)

October 2015

1977 Cancer Gene Panel. This file lists all 1,977 genes in the Cancer Gene Panel, used in this study...

Additional file 1: of HDAC is indispensable for IFN-γ-induced B7-H1 expression in gastric cancer

Rui Deng (157986)
Peng Zhang (2071)
Weizhen Liu (1418449)
Xiangyu Zeng (6075611)
Xianxiong Ma (4276441)
Liang Shi (8078)
Tao Wang (12008)
Yuping Yin (3617510)
Weilong Chang (838939)
Pei Zhang (232846)
Guobin Wang (322861)
Kaixiong Tao (281715)

December 2018

Figure S1. HDAC1–3 expression correlated B7-H1 expression in clinical gastric specimens. (A) B7-H1 a...

Additional file 3: Table S4. of IL-10 and integrin signaling pathways are associated with head and neck cancer progression

Sophia Bornstein (3515549)
Mark Schmidt (3172602)
Gabrielle Choonoo (3325773)
Trevor Levin (755264)
Joe Gray (94862)
Charles Thomas (1871524)
Melissa Wong (3032583)
Shannon McWeeney (39058)

January 2016

Pathways significantly enriched for differentially expressed (DE) genes between TCGA HNSCC progresso...

Additional file 3: Table S2. of A kinome siRNA screen identifies HGS as a potential target for liver cancers with oncogenic mutations in CTNNB1

Frédéric Canal (3179895)
Elodie Anthony (3461654)
Aurianne Lescure (310453)
Elaine Del Nery (310455)
Jacques Camonis (49694)
Franck Perez (259284)
Bruno Ragazzon (140444)
Christine Perret (365234)

December 2015

List of the 52 genes identified among the 687 tested genes in HT screening as important for the cell...

Additional file 6: of The molecular landscape of premenopausal breast cancer

Serena Liao (3582692)
Ryan Hartmaier (109111)
Kandace McGuire (3582695)
Shannon Puhalla (3582689)
Soumya Luthra (732484)
Uma Chandran (732485)
Tianzhou Ma (3582698)
Rohit Bhargava (562035)
Francesmary Modugno (757958)
Nancy Davidson (3512738)
Steve Benz (3582686)
Adrian Lee (3161067)
George Tseng (150934)
Steffi Oesterreich (109122)

August 2015

The Cancer Genome Atlas (TCGA) Ingenuity pathway analysis (IPA) upstream regulators. Table S1., Tabl...

Additional file 3: Table S1. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Abstract

Extracted data

Additional file 3: Table S1. of HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

Abstract

Extracted data

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