Additional file 2: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Additional file 2: of Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

Kelly Robinson (3693385)
Jonathan Crabtree (80659)
John Mattick (544773)
Kathleen Anderson (3693382)
Julie Dunning Hotopp (579385)

January 2017

This file is a tab-delimited text file of all TCGA read pairs and their corresponding metadata and b...

Additional file 1: of The impact of pharmacokinetic gene profiles across human cancers

Michael Zimmermann (203279)
Terry Therneau (5245403)
Jean-Pierre Kocher (179225)

May 2018

PK gene profiles across human cancers. This file contains additional text and figures that support t...

Additional file 3: Table S3. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâgenomic driver associations

HoJoon Lee (3581495)
Jennifer Palm (3581492)
Susan Grimes (215227)
Hanlee Ji (29919)

October 2015

The number of genes selected from TCGA studies by type of genetic alterations and cancer type. (XLSX...

Additional file 1: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

David Tamborero (280874)
Carlota Rubio-Perez (3537731)
Jordi Deu-Pons (3464579)
Michael Schroeder (10133)
Ana Vivancos (646007)
Ana Rovira (163968)
Ignasi Tusquets (58580)
Joan Albanell (163974)
Jordi Rodon (201558)
Josep Tabernero (237681)
Carmen de Torres (122811)
Rodrigo Dienstmann (5038079)
Abel Gonzalez-Perez (280875)
Nuria Lopez-Bigas (1759)

March 2018

Table S1. The features provided by different resources/methods and details about which of them are e...

Additional file 1: of Pan-cancer analysis of tumor metabolic landscape associated with genomic alterations

Hongyoon Choi (541919)
Kwon Na (5867924)

October 2018

Materials and methods, supplementary figures and supplementary tables. (PDF 1650 kb

Additional file 2: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Zhuyi Xue (5514434)
René Warren (5431511)
Ewan Gibb (5514431)
Daniel MacMillan (5514440)
Johnathan Wong (5514425)
Readman Chiu (41422)
S. Austin Hammond (762521)
Chen Yang (207381)
Ka Nip (5514428)
Catherine Ennis (5514437)
Abigail Hahn (5514422)
Sheila Reynolds (4693027)
Inanc Birol (277074)

July 2018

Supplementary tables. It includes all supplementary tables. Table S1.List of 114 cancer-related gene...

Additional file 1: Table S1. of Integrating cancer genomic data into electronic health records

Jeremy Warner (3561563)
Sandeep Jain (497319)
Mia Levy (3561566)

October 2016

Nomenclatures of relevance to genomic medicine. Table S2. Terminology systems that uniquely identify...

Additional file 1: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Zhuyi Xue (5514434)
René Warren (5431511)
Ewan Gibb (5514431)
Daniel MacMillan (5514440)
Johnathan Wong (5514425)
Readman Chiu (41422)
S. Austin Hammond (762521)
Chen Yang (207381)
Ka Nip (5514428)
Catherine Ennis (5514437)
Abigail Hahn (5514422)
Sheila Reynolds (4693027)
Inanc Birol (277074)

July 2018

Supplementary figures. It includes all supplementary figures except Figure S4. Figure S1. Benchmark ...

Additional file 2: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Table S1. Systems-level properties of cancer genes. Table S2 List of 273 publications describing can...

Additional file 1: of MUFFINN: cancer gene discovery via network analysis of somatic mutation data

Ara Cho (1736176)
Jung Shim (3418757)
Eiru Kim (707696)
Fran Supek (105927)
Ben Lehner (4828)
Insuk Lee (41276)

June 2016

Supplementary online information including supplementary Figures S1âS9 and supplementary Table S1....

Additional file 1: of The genomic road to invasionâexamining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples

Henry Wood (482871)
Catherine Daly (482869)
Rebecca Chalkley (4094965)
Burcu Senguven (4094971)
Lisa Ross (4094980)
Philip Egan (482866)
Preetha Chengot (4094959)
Jennifer Graham (4094962)
Neeraj Sethi (4094974)
Thian Ong (4094977)
Kenneth MacLennan (4094968)
Pamela Rabbitts (482875)
Caroline Conway (482868)

June 2017

An example of tissue selection, a full sample list, exome sequencing metrics, full VAF and neutralit...

Additional file 2: of Rational design of cancer gene panels with OncoPaD

Carlota Rubio-Perez (3537731)
Jordi Deu-Pons (3464579)
David Tamborero (280874)
Nuria Lopez-Bigas (1759)
Abel Gonzalez-Perez (280875)

October 2016

Supplementary Data. PDF file containing the headers and legends of Tables S1âS3, Figures S1 and S2...

Additional file 2: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S2. A. Number of CDGs mutated in at least 5 samples with methylation data in one tumor type; B...

Additional file 1: of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Andrew Uzilov (840952)
Wei Ding (690)
Marc Fink (3440288)
Yevgeniy Antipin (88148)
Andrew Brohl (3440327)
Claire Davis (3440309)
Chun Lau (3440342)
Chetanya Pandya (2158300)
Hardik Shah (3384089)
Yumi Kasai (25927)
James Powell (307938)
Mark Micchelli (3440306)
Rafael Castellanos (3440336)
Zhongyang Zhang (828677)
Michael Linderman (171683)
Yayoi Kinoshita (324653)
Micol Zweig (3440330)
Katie Raustad (3440339)
Kakit Cheung (3440315)
Diane Castillo (3440285)
Melissa Wooten (840951)
Imane Bourzgui (3440333)
Leah Newman (3440345)
Gintaras Deikus (2662735)
Bino Mathew (3440300)
Jun Zhu (84054)
Benjamin Glicksberg (3440291)
Aye Moe (3440312)
Jun Liao (1402627)
Lisa Edelmann (2633281)
Joel Dudley (3440297)
Robert Maki (3440294)
Andrew Kasarskis (6291)
Randall Holcombe (3440324)
Milind Mahajan (106624)
Ke Hao (50181)
Boris Reva (88147)
Janina Longtine (3440321)
Daniela Starcevic (3440303)
Robert Sebra (840947)
Michael Donovan (3440318)
Shuyu Li (18735)
Eric Schadt (105785)
Rong Chen (29176)

June 2016

Supplementary Tables: Tables S1-S11. See Additional file 2 for detailed table legends. (XLSX 144 kb

Additional file 3: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Text S1. Details with some modified steps for identifying EDGs.; Results of MDGs in LGG; Results fro...

Additional file 2: of Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

Kelly Robinson (3693385)
Jonathan Crabtree (80659)
John Mattick (544773)
Kathleen Anderson (3693382)
Julie Dunning Hotopp (579385)

January 2017

This file is a tab-delimited text file of all TCGA read pairs and their corresponding metadata and b...

Additional file 1: of The impact of pharmacokinetic gene profiles across human cancers

Michael Zimmermann (203279)
Terry Therneau (5245403)
Jean-Pierre Kocher (179225)

May 2018

PK gene profiles across human cancers. This file contains additional text and figures that support t...

Additional file 3: Table S3. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâgenomic driver associations

HoJoon Lee (3581495)
Jennifer Palm (3581492)
Susan Grimes (215227)
Hanlee Ji (29919)

October 2015

The number of genes selected from TCGA studies by type of genetic alterations and cancer type. (XLSX...

Additional file 1: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

David Tamborero (280874)
Carlota Rubio-Perez (3537731)
Jordi Deu-Pons (3464579)
Michael Schroeder (10133)
Ana Vivancos (646007)
Ana Rovira (163968)
Ignasi Tusquets (58580)
Joan Albanell (163974)
Jordi Rodon (201558)
Josep Tabernero (237681)
Carmen de Torres (122811)
Rodrigo Dienstmann (5038079)
Abel Gonzalez-Perez (280875)
Nuria Lopez-Bigas (1759)

March 2018

Table S1. The features provided by different resources/methods and details about which of them are e...

Additional file 1: of Pan-cancer analysis of tumor metabolic landscape associated with genomic alterations

Hongyoon Choi (541919)
Kwon Na (5867924)

October 2018

Materials and methods, supplementary figures and supplementary tables. (PDF 1650 kb

Additional file 2: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Zhuyi Xue (5514434)
René Warren (5431511)
Ewan Gibb (5514431)
Daniel MacMillan (5514440)
Johnathan Wong (5514425)
Readman Chiu (41422)
S. Austin Hammond (762521)
Chen Yang (207381)
Ka Nip (5514428)
Catherine Ennis (5514437)
Abigail Hahn (5514422)
Sheila Reynolds (4693027)
Inanc Birol (277074)

July 2018

Supplementary tables. It includes all supplementary tables. Table S1.List of 114 cancer-related gene...

Additional file 1: Table S1. of Integrating cancer genomic data into electronic health records

Jeremy Warner (3561563)
Sandeep Jain (497319)
Mia Levy (3561566)

October 2016

Nomenclatures of relevance to genomic medicine. Table S2. Terminology systems that uniquely identify...

Additional file 1: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Zhuyi Xue (5514434)
René Warren (5431511)
Ewan Gibb (5514431)
Daniel MacMillan (5514440)
Johnathan Wong (5514425)
Readman Chiu (41422)
S. Austin Hammond (762521)
Chen Yang (207381)
Ka Nip (5514428)
Catherine Ennis (5514437)
Abigail Hahn (5514422)
Sheila Reynolds (4693027)
Inanc Birol (277074)

July 2018

Supplementary figures. It includes all supplementary figures except Figure S4. Figure S1. Benchmark ...

Additional file 2: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Table S1. Systems-level properties of cancer genes. Table S2 List of 273 publications describing can...

Additional file 1: of MUFFINN: cancer gene discovery via network analysis of somatic mutation data

Ara Cho (1736176)
Jung Shim (3418757)
Eiru Kim (707696)
Fran Supek (105927)
Ben Lehner (4828)
Insuk Lee (41276)

June 2016

Supplementary online information including supplementary Figures S1âS9 and supplementary Table S1....

Additional file 1: of The genomic road to invasionâexamining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples

Henry Wood (482871)
Catherine Daly (482869)
Rebecca Chalkley (4094965)
Burcu Senguven (4094971)
Lisa Ross (4094980)
Philip Egan (482866)
Preetha Chengot (4094959)
Jennifer Graham (4094962)
Neeraj Sethi (4094974)
Thian Ong (4094977)
Kenneth MacLennan (4094968)
Pamela Rabbitts (482875)
Caroline Conway (482868)

June 2017

An example of tissue selection, a full sample list, exome sequencing metrics, full VAF and neutralit...

Additional file 2: of Rational design of cancer gene panels with OncoPaD

Carlota Rubio-Perez (3537731)
Jordi Deu-Pons (3464579)
David Tamborero (280874)
Nuria Lopez-Bigas (1759)
Abel Gonzalez-Perez (280875)

October 2016

Supplementary Data. PDF file containing the headers and legends of Tables S1âS3, Figures S1 and S2...

Additional file 2: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S2. A. Number of CDGs mutated in at least 5 samples with methylation data in one tumor type; B...

Additional file 1: of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Andrew Uzilov (840952)
Wei Ding (690)
Marc Fink (3440288)
Yevgeniy Antipin (88148)
Andrew Brohl (3440327)
Claire Davis (3440309)
Chun Lau (3440342)
Chetanya Pandya (2158300)
Hardik Shah (3384089)
Yumi Kasai (25927)
James Powell (307938)
Mark Micchelli (3440306)
Rafael Castellanos (3440336)
Zhongyang Zhang (828677)
Michael Linderman (171683)
Yayoi Kinoshita (324653)
Micol Zweig (3440330)
Katie Raustad (3440339)
Kakit Cheung (3440315)
Diane Castillo (3440285)
Melissa Wooten (840951)
Imane Bourzgui (3440333)
Leah Newman (3440345)
Gintaras Deikus (2662735)
Bino Mathew (3440300)
Jun Zhu (84054)
Benjamin Glicksberg (3440291)
Aye Moe (3440312)
Jun Liao (1402627)
Lisa Edelmann (2633281)
Joel Dudley (3440297)
Robert Maki (3440294)
Andrew Kasarskis (6291)
Randall Holcombe (3440324)
Milind Mahajan (106624)
Ke Hao (50181)
Boris Reva (88147)
Janina Longtine (3440321)
Daniela Starcevic (3440303)
Robert Sebra (840947)
Michael Donovan (3440318)
Shuyu Li (18735)
Eric Schadt (105785)
Rong Chen (29176)

June 2016

Supplementary Tables: Tables S1-S11. See Additional file 2 for detailed table legends. (XLSX 144 kb

Additional file 3: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Text S1. Details with some modified steps for identifying EDGs.; Results of MDGs in LGG; Results fro...

Additional file 2: of Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

Kelly Robinson (3693385)
Jonathan Crabtree (80659)
John Mattick (544773)
Kathleen Anderson (3693382)
Julie Dunning Hotopp (579385)

January 2017

This file is a tab-delimited text file of all TCGA read pairs and their corresponding metadata and b...

Additional file 1: of The impact of pharmacokinetic gene profiles across human cancers

Michael Zimmermann (203279)
Terry Therneau (5245403)
Jean-Pierre Kocher (179225)

May 2018

PK gene profiles across human cancers. This file contains additional text and figures that support t...

Additional file 3: Table S3. of The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinicalâgenomic driver associations

HoJoon Lee (3581495)
Jennifer Palm (3581492)
Susan Grimes (215227)
Hanlee Ji (29919)

October 2015

The number of genes selected from TCGA studies by type of genetic alterations and cancer type. (XLSX...

Additional file 2: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Abstract

Extracted data

Additional file 2: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Abstract

Extracted data

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