Additional file 1: of Landscape of gene fusions in epithelial cancers: seq and ye shall find

Chandan Kumar-Sinha (228759)
Shanker Kalyana-Sundaram (2734888)
Arul Chinnaiyan (2032537)

Publication date

December 2015

DOI

10.6084/m9.figshare.c.3644912_d2.v1

Abstract

Recurrent gene fusions in epithelial cancers. Summary of recurrent gene fusions in epithelial carcinoma across different tissues. a Gene fusions with common 5′ and 3′ genes. b Multiple 5′ partners with common 3′ genes. c Common 5′ gene partners with multiple 3′ genes. (DOCX 25 kb

Extracted data

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Additional file 1: of Landscape of gene fusions in epithelial cancers: seq and ye shall find

Chandan Kumar-Sinha (228759)
Shanker Kalyana-Sundaram (2734888)
Arul Chinnaiyan (2032537)

Open link

Publication date

December 2015

DOI

10.6084/m9.figshare.c.3644912_d2.v1

Abstract

Extracted data

Topics

carcinomaDisease

geneOrganisation

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

November 2018

Figure S1. Mutation patterns of the identified 32 MDGs across 20 TCGA tumor types. Each row represen...

Additional file 3: 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

Lists of all cancer genes, known cancer genes, and candidate cancer genes. (XLSX 840 kb

Additional file 1: of Targeted sequencing of circulating cell-free DNA in stage II-III resectable oesophageal squamous cell carcinoma patients

Meng, Pei
Wei, Jiacong
Geng, Yiqun
Chen, Shaobin
Terpstra, Miente Martijn
Huang, Qiongyi
Zhang, Qian
Su, Zuoqing
Yu, Wanchun
Su, Min
Kok, Klaas
van den Berg, Anke
Gu, Jiang
Translational Immunology Groningen (TRIGR)
Stem Cell Aging Leukemia and Lymphoma (SALL)
Guided Treatment in Optimal Selected Cancer Patients (GUTS)
Shantou University Medical College

August 2019

Overview of the 483 genes present in the Illumina cancer gene panel. (XLSX 14 kb

Additional file 1 of Integrating mutation and gene expression cross-sectional data to infer cancer progression

Julia Fleck (3491156)
Ana Pavel (3491159)
Christos Cassandras (3491153)

January 2016

The partition of 72 mutation and 319 expression genes in 3 phases of cancer progression. The values ...

Additional file 7: Figure S3. of Transcriptome analysis of paired primary colorectal carcinoma and liver metastases reveals fusion transcripts and similar gene expression profiles in primary carcinoma and liver metastases

Ja-Rang Lee (3485255)
Chae Kwon (3485243)
Yuri Choi (1715992)
Hye Park (3485240)
Hyun Kim (127301)
Hong-Jae Jo (3485249)
Nahmgun Oh (3485246)
Do Park (3485252)

July 2016

Fusion transcripts in validation sets. (A) Gene fusion between ZMYND8 and SEPT9 gene by interchromos...

Additional file 1: of Additional germline findings from a tumor profiling program

Neda Stjepanovic (5618591)
Tracy Stockley (3421913)
Philippe Bedard (362729)
Jeanna McCuaig (5618594)
Melyssa Aronson (5618597)
Spring Holter (5618600)
Kara Semotiuk (5618603)
Natasha Leighl (703141)
Raymond Jang (5618606)
Monika Krzyzanowska (3421910)
Amit Oza (3421889)
Abha Gupta (3902173)
Christine Elser (5618618)
Lailah Ahmed (5618627)
Lisa Wang (3046971)
Suzanne Kamel-Reid (3421898)
Lillian Siu (3421904)
Raymond Kim (3421883)

August 2018

Table S1. 48 genes included in the TruSeq Amplicon Cancer Panel (TSACP, Illumina), which includes 21...

Additional file 1: of Clonal relatedness in tumour pairs of breast cancer patients

Jana Biermann (5618684)
Toshima Parris (3762496)
Szilรกrd Nemes (5618741)
Anna Danielsson (172641)
Hanna Engqvist (5618690)
Elisabeth Werner Rรถnnerman (5618744)
Eva Forssell-Aronsson (658141)
Anikรณ Kovรกcs (5618747)
Per Karlsson (48671)
Khalil Helou (561963)

August 2018

Supplementary Methods. Description of nucleic acid isolation and purification, aCGH gene expression ...

Additional file 2: of Predominance of triple wild-type and IGF2R mutations in mucosal melanomas

Yuuki Iida (5907662)
Matthew Salomon (3578312)
Keisuke Hata (510174)
Kevin Tran (519050)
Shuichi Ohe (5907671)
Chester Griffiths (5907674)
Sandy Hsu (117448)
Nellie Nelson (5907677)
Dave Hoon (5229374)

October 2018

Gene List for Haloplex. Description of the genes targeted in the Haloplex pannel including, gene nam...

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 8: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

The schematic diagram of other fused genes. A figure showing how the rest of gene fusions occurred. ...

Additional file 3: of Liver cancer cell lines distinctly mimic the metabolic gene expression pattern of the corresponding human tumours

Zeribe Nwosu (5711912)
Nadia Battello (3551528)
Melanie Rothley (3179106)
Weronika PioroĹska (5711921)
Barbara Sitek (522367)
Matthias Ebert (170342)
Ute Hofmann (204608)
Jonathan Sleeman (144047)
Stefan WĂślfl (5711924)
Christoph Meyer (1428763)
Dominik Megger (5711918)
Steven Dooley (194854)

September 2018

Table S2. HCC-associated genes. Contains a set of genes often associated with HCC, including those r...

Additional file 2: of Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

A. Barutcu (3490721)
Bryan Lajoie (3481844)
Rachel McCord (3490733)
Coralee Tye (3490730)
Deli Hong (3490739)
Terri Messier (3490724)
Gillian Browne (3490727)
Andre van Wijnen (3476351)
Jane Lian (3490736)
Janet Stein (2267158)
Job Dekker (48174)
Anthony Imbalzano (3490742)
Gary Stein (2267170)

September 2015

A table listing the gene ontology terms of differentially expressed genes between MCF-10A and MCF-7 ...

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 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...

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

November 2018

Figure S1. Mutation patterns of the identified 32 MDGs across 20 TCGA tumor types. Each row represen...

Additional file 3: 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

Lists of all cancer genes, known cancer genes, and candidate cancer genes. (XLSX 840 kb

Additional file 1: of Targeted sequencing of circulating cell-free DNA in stage II-III resectable oesophageal squamous cell carcinoma patients

Meng, Pei
Wei, Jiacong
Geng, Yiqun
Chen, Shaobin
Terpstra, Miente Martijn
Huang, Qiongyi
Zhang, Qian
Su, Zuoqing
Yu, Wanchun
Su, Min
Kok, Klaas
van den Berg, Anke
Gu, Jiang
Translational Immunology Groningen (TRIGR)
Stem Cell Aging Leukemia and Lymphoma (SALL)
Guided Treatment in Optimal Selected Cancer Patients (GUTS)
Shantou University Medical College

August 2019

Overview of the 483 genes present in the Illumina cancer gene panel. (XLSX 14 kb

Ja-Rang Lee (3485255)
Chae Kwon (3485243)
Yuri Choi (1715992)
Hye Park (3485240)
Hyun Kim (127301)
Hong-Jae Jo (3485249)
Nahmgun Oh (3485246)
Do Park (3485252)

July 2016

Fusion transcripts in validation sets. (A) Gene fusion between ZMYND8 and SEPT9 gene by interchromos...

Additional file 1: of Additional germline findings from a tumor profiling program

Neda Stjepanovic (5618591)
Tracy Stockley (3421913)
Philippe Bedard (362729)
Jeanna McCuaig (5618594)
Melyssa Aronson (5618597)
Spring Holter (5618600)
Kara Semotiuk (5618603)
Natasha Leighl (703141)
Raymond Jang (5618606)
Monika Krzyzanowska (3421910)
Amit Oza (3421889)
Abha Gupta (3902173)
Christine Elser (5618618)
Lailah Ahmed (5618627)
Lisa Wang (3046971)
Suzanne Kamel-Reid (3421898)
Lillian Siu (3421904)
Raymond Kim (3421883)

August 2018

Table S1. 48 genes included in the TruSeq Amplicon Cancer Panel (TSACP, Illumina), which includes 21...

Additional file 1: of Clonal relatedness in tumour pairs of breast cancer patients

Jana Biermann (5618684)
Toshima Parris (3762496)
Szilรกrd Nemes (5618741)
Anna Danielsson (172641)
Hanna Engqvist (5618690)
Elisabeth Werner Rรถnnerman (5618744)
Eva Forssell-Aronsson (658141)
Anikรณ Kovรกcs (5618747)
Per Karlsson (48671)
Khalil Helou (561963)

August 2018

Supplementary Methods. Description of nucleic acid isolation and purification, aCGH gene expression ...

Additional file 2: of Predominance of triple wild-type and IGF2R mutations in mucosal melanomas

Yuuki Iida (5907662)
Matthew Salomon (3578312)
Keisuke Hata (510174)
Kevin Tran (519050)
Shuichi Ohe (5907671)
Chester Griffiths (5907674)
Sandy Hsu (117448)
Nellie Nelson (5907677)
Dave Hoon (5229374)

October 2018

Gene List for Haloplex. Description of the genes targeted in the Haloplex pannel including, gene nam...

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 8: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

The schematic diagram of other fused genes. A figure showing how the rest of gene fusions occurred. ...

Additional file 3: of Liver cancer cell lines distinctly mimic the metabolic gene expression pattern of the corresponding human tumours

Zeribe Nwosu (5711912)
Nadia Battello (3551528)
Melanie Rothley (3179106)
Weronika PioroĹska (5711921)
Barbara Sitek (522367)
Matthias Ebert (170342)
Ute Hofmann (204608)
Jonathan Sleeman (144047)
Stefan WĂślfl (5711924)
Christoph Meyer (1428763)
Dominik Megger (5711918)
Steven Dooley (194854)

September 2018

Table S2. HCC-associated genes. Contains a set of genes often associated with HCC, including those r...

Additional file 2: of Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

A. Barutcu (3490721)
Bryan Lajoie (3481844)
Rachel McCord (3490733)
Coralee Tye (3490730)
Deli Hong (3490739)
Terri Messier (3490724)
Gillian Browne (3490727)
Andre van Wijnen (3476351)
Jane Lian (3490736)
Janet Stein (2267158)
Job Dekker (48174)
Anthony Imbalzano (3490742)
Gary Stein (2267170)

September 2015

A table listing the gene ontology terms of differentially expressed genes between MCF-10A and MCF-7 ...

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...

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...

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

November 2018

Figure S1. Mutation patterns of the identified 32 MDGs across 20 TCGA tumor types. Each row represen...

Additional file 3: 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

Lists of all cancer genes, known cancer genes, and candidate cancer genes. (XLSX 840 kb

Additional file 1: of Targeted sequencing of circulating cell-free DNA in stage II-III resectable oesophageal squamous cell carcinoma patients

Meng, Pei
Wei, Jiacong
Geng, Yiqun
Chen, Shaobin
Terpstra, Miente Martijn
Huang, Qiongyi
Zhang, Qian
Su, Zuoqing
Yu, Wanchun
Su, Min
Kok, Klaas
van den Berg, Anke
Gu, Jiang
Translational Immunology Groningen (TRIGR)
Stem Cell Aging Leukemia and Lymphoma (SALL)
Guided Treatment in Optimal Selected Cancer Patients (GUTS)
Shantou University Medical College

August 2019

Overview of the 483 genes present in the Illumina cancer gene panel. (XLSX 14 kb

Additional file 1: of Landscape of gene fusions in epithelial cancers: seq and ye shall find

Abstract

Extracted data

Additional file 1: of Landscape of gene fusions in epithelial cancers: seq and ye shall find

Abstract

Extracted data

Topics

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Topics

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