Additional file 8: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Additional file 4: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

r Table S4. Significantly differentially expressed genes without somatic mutations. (XLSX 272 kb

Proteomic analysis of human prostate cancer PC-3M-1E8 cells and PC-3M-2B4 cells of same origin but with different metastatic potential

Shujiang Zhang (5917007)
Chengcheng Zheng (5917010)
Shunheng Yao (5917013)
Zhonghui Wang (4089880)
Li Xu (108702)
Rongfu Yang (5917016)
Xiang Meng (383515)
Jianhui Wu (385334)
Li Zhou (54356)
Zuyue Sun (5917019)

October 2018

Prostate cancer (PCa) is the second most frequently diagnosed cancer and the fifth leading cause of ...

Additional file 2: of Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles

Robin Imperial (6113699)
Zaheer Ahmed (2471398)
Omer Toor (6113702)
Cihat ErdoÄan (6113705)
Ateeq Khaliq (6113708)
Paul Case (6113711)
James Case (6113714)
Kevin Kennedy (40172)
Lee Cummings (6113717)
Niklas Melton (6113720)
Shahzad Raza (6113723)
Banu Diri (4598581)
Ramzi Mohammad (3520061)
Bassel El-Rayes (4006997)
Timothy Pluard (6113726)
Arif Hussain (226527)
Janakiraman Subramanian (5150669)
Ashiq Masood (6113729)

December 2018

Inclusion and exclusion criteria for somatic mutation analysis. MSI-H, POLE mutation samples, rectos...

Additional file 7: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

Reproducibility of Protein Fold Changes among Biological Replicates. This figure shows the log2 fold...

Additional file 2: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

MA Plot. This MA plot shows the data before (a) and after (b) transformation. The variances of the d...

Additional file 4: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

TCGA PRAD DEPs Protein and mRNA Expression Data. This spreadsheet contains the patient demographics,...

Additional file 9: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S7. Table comparing relevant germline alterations, presented here, with other publications. (X...

Additional file 2: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S1. Detailed overview of the capture designs and targeted regions. (XLSX 974 kb

Additional file 1: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S1. DNA damage response gene variants in prostate cancer cell lines. (XLSX 16 kb

Additional file 7: of Metabolic reprogramming-based characterization of circulating tumor cells in prostate cancer

Jing Chen (4762)
Shunwang Cao (5338076)
Bo Situ (4682563)
Juan Zhong (486982)
Yanwei Hu (766578)
Shufen Li (746508)
Jinlan Huang (4615594)
Jiasen Xu (729951)
Shiyang Wu (729947)
Jinduan Lin (5338073)
Qianwen Zhao (5467433)
Zhen Cai (576458)
Lei Zheng (106363)
Qian Wang (32718)

June 2018

Figure S2. Functions of the differentially expressed genes in glucose and glycogen metabolism. These...

Additional file 2: Table S1. of Distinct prostate cancer-related mRNA cargo in extracellular vesicle subsets from prostate cell lines

Elisa Lázaro-Ibáñez (573049)
Taral Lunavat (3706165)
Su Jang (3706168)
Carmen Escobedo-Lucea (431976)
Jorge Oliver-De La Cruz (573045)
Pia Siljander (293504)
Jan Lötvall (84140)
Marjo Yliperttula (148514)

February 2017

Top Regulated Genes: Distinctly different genes between LNCaP MVs vs PNT2 MVs. (XLSX 9 kb

Additional file 2 of Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

Tingting Gong (540807)
Weerachai Jaratlerdsiri (519605)
Jue Jiang (6565325)
Cali Willet (3456962)
Tracy Chew (8901187)
Sean M. Patrick (13559456)
Ruth J. Lyons (13559459)
Anne-Maree Haynes (5706494)
Gabriela Pasqualim (688774)
Ilma Simoni Brum (5540651)
Phillip D. Stricker (5706485)
Shingai B. A. Mutambirwa (13559462)
Rosemarie Sadsad (495058)
Anthony T. Papenfuss (9450362)
Riana M. S. Bornman (13559465)
Eva K. F. Chan (9311796)
Vanessa M. Hayes (13559468)

August 2022

Additional file 2: Table S4. Summary of gene fusions identified from SVs. Table S5. SV calls resulti...

Additional file 2: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S2. Potential deleterious alterations of DNA damage response genes in prostate cancer cell lin...

Additional file 4: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Figure S1. Standard GSEA plots of the HALLMARK_ANDROGEN_RESPONSE gene set. Analysis included pre-ran...

Additional file 4: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S3. Overview of which samples that were sequenced with which capture design. (XLSX 123 kb

Additional file 4: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

r Table S4. Significantly differentially expressed genes without somatic mutations. (XLSX 272 kb

Proteomic analysis of human prostate cancer PC-3M-1E8 cells and PC-3M-2B4 cells of same origin but with different metastatic potential

Shujiang Zhang (5917007)
Chengcheng Zheng (5917010)
Shunheng Yao (5917013)
Zhonghui Wang (4089880)
Li Xu (108702)
Rongfu Yang (5917016)
Xiang Meng (383515)
Jianhui Wu (385334)
Li Zhou (54356)
Zuyue Sun (5917019)

October 2018

Prostate cancer (PCa) is the second most frequently diagnosed cancer and the fifth leading cause of ...

Additional file 2: of Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles

Robin Imperial (6113699)
Zaheer Ahmed (2471398)
Omer Toor (6113702)
Cihat ErdoÄan (6113705)
Ateeq Khaliq (6113708)
Paul Case (6113711)
James Case (6113714)
Kevin Kennedy (40172)
Lee Cummings (6113717)
Niklas Melton (6113720)
Shahzad Raza (6113723)
Banu Diri (4598581)
Ramzi Mohammad (3520061)
Bassel El-Rayes (4006997)
Timothy Pluard (6113726)
Arif Hussain (226527)
Janakiraman Subramanian (5150669)
Ashiq Masood (6113729)

December 2018

Inclusion and exclusion criteria for somatic mutation analysis. MSI-H, POLE mutation samples, rectos...

Additional file 7: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

Reproducibility of Protein Fold Changes among Biological Replicates. This figure shows the log2 fold...

Additional file 2: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

MA Plot. This MA plot shows the data before (a) and after (b) transformation. The variances of the d...

Additional file 4: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

TCGA PRAD DEPs Protein and mRNA Expression Data. This spreadsheet contains the patient demographics,...

Additional file 9: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S7. Table comparing relevant germline alterations, presented here, with other publications. (X...

Additional file 2: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S1. Detailed overview of the capture designs and targeted regions. (XLSX 974 kb

Additional file 1: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S1. DNA damage response gene variants in prostate cancer cell lines. (XLSX 16 kb

Additional file 7: of Metabolic reprogramming-based characterization of circulating tumor cells in prostate cancer

Jing Chen (4762)
Shunwang Cao (5338076)
Bo Situ (4682563)
Juan Zhong (486982)
Yanwei Hu (766578)
Shufen Li (746508)
Jinlan Huang (4615594)
Jiasen Xu (729951)
Shiyang Wu (729947)
Jinduan Lin (5338073)
Qianwen Zhao (5467433)
Zhen Cai (576458)
Lei Zheng (106363)
Qian Wang (32718)

June 2018

Figure S2. Functions of the differentially expressed genes in glucose and glycogen metabolism. These...

Additional file 2: Table S1. of Distinct prostate cancer-related mRNA cargo in extracellular vesicle subsets from prostate cell lines

Elisa Lázaro-Ibáñez (573049)
Taral Lunavat (3706165)
Su Jang (3706168)
Carmen Escobedo-Lucea (431976)
Jorge Oliver-De La Cruz (573045)
Pia Siljander (293504)
Jan Lötvall (84140)
Marjo Yliperttula (148514)

February 2017

Top Regulated Genes: Distinctly different genes between LNCaP MVs vs PNT2 MVs. (XLSX 9 kb

Additional file 2 of Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

Tingting Gong (540807)
Weerachai Jaratlerdsiri (519605)
Jue Jiang (6565325)
Cali Willet (3456962)
Tracy Chew (8901187)
Sean M. Patrick (13559456)
Ruth J. Lyons (13559459)
Anne-Maree Haynes (5706494)
Gabriela Pasqualim (688774)
Ilma Simoni Brum (5540651)
Phillip D. Stricker (5706485)
Shingai B. A. Mutambirwa (13559462)
Rosemarie Sadsad (495058)
Anthony T. Papenfuss (9450362)
Riana M. S. Bornman (13559465)
Eva K. F. Chan (9311796)
Vanessa M. Hayes (13559468)

August 2022

Additional file 2: Table S4. Summary of gene fusions identified from SVs. Table S5. SV calls resulti...

Additional file 2: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S2. Potential deleterious alterations of DNA damage response genes in prostate cancer cell lin...

Additional file 4: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Figure S1. Standard GSEA plots of the HALLMARK_ANDROGEN_RESPONSE gene set. Analysis included pre-ran...

Additional file 4: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S3. Overview of which samples that were sequenced with which capture design. (XLSX 123 kb

Additional file 4: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

r Table S4. Significantly differentially expressed genes without somatic mutations. (XLSX 272 kb

Proteomic analysis of human prostate cancer PC-3M-1E8 cells and PC-3M-2B4 cells of same origin but with different metastatic potential

Shujiang Zhang (5917007)
Chengcheng Zheng (5917010)
Shunheng Yao (5917013)
Zhonghui Wang (4089880)
Li Xu (108702)
Rongfu Yang (5917016)
Xiang Meng (383515)
Jianhui Wu (385334)
Li Zhou (54356)
Zuyue Sun (5917019)

October 2018

Prostate cancer (PCa) is the second most frequently diagnosed cancer and the fifth leading cause of ...

Additional file 2: of Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles

Robin Imperial (6113699)
Zaheer Ahmed (2471398)
Omer Toor (6113702)
Cihat ErdoÄan (6113705)
Ateeq Khaliq (6113708)
Paul Case (6113711)
James Case (6113714)
Kevin Kennedy (40172)
Lee Cummings (6113717)
Niklas Melton (6113720)
Shahzad Raza (6113723)
Banu Diri (4598581)
Ramzi Mohammad (3520061)
Bassel El-Rayes (4006997)
Timothy Pluard (6113726)
Arif Hussain (226527)
Janakiraman Subramanian (5150669)
Ashiq Masood (6113729)

December 2018

Inclusion and exclusion criteria for somatic mutation analysis. MSI-H, POLE mutation samples, rectos...

Additional file 8: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Abstract

Extracted data

Additional file 8: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Abstract

Extracted data

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