Additional file 8: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Additional file 8 of An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping

Gayathri Thillaiyampalam (4711104)
Fabio Liberante (4711101)
Liam Murray (584595)
Chris Cardwell (4676743)
Ken Mills (204775)
Shu-Dong Zhang (231229)

December 2017

Tumor vs Normal 5 sub-gene signatures. The 5 non-joint 83-gene signatures are included, each consist...

Additional file 2: Table S7. of Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer

Guanglong Jiang (3469451)
Shijun Zhang (123373)
Aida Yazdanparast (3469457)
Meng Li (79487)
Aniruddha Pawar (3469454)
Yunlong Liu (46477)
Sai Inavolu (3469448)
Lijun Cheng (3469445)

August 2016

Correlation coefficient r across 4 genomics level comparison in breast cancer. (XLSX 1527 kb

Additional file 5 of An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping

Gayathri Thillaiyampalam (4711104)
Fabio Liberante (4711101)
Liam Murray (584595)
Chris Cardwell (4676743)
Ken Mills (204775)
Shu-Dong Zhang (231229)

December 2017

Tumor vs Adjacent differentially expressed genes. The full list of 164 significant genes selected fr...

Additional file 9: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S7. Proteins (nâ=â285) whose abundance in breast tumors correlated with tumor grade. (XLS...

Additional file 7: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S5. Significantly differentially expressed proteins between breast tumors and adjacent non-ca...

Additional file 12: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S10. Concordance values (rho) for 5677 protein-mRNA pairs in breast tumors (nâ=â59). (XLS...

Additional file 10: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S8. Proliferation score and global protein-mRNA concordance values for 59 breast tumors. (XLS...

Additional file 4: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S2. Enrichment of differently expressed protein-coding genes in KEGG pathways (tumor vs. adja...

Additional file 6: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S4. Most differentially expressed proteins between LumA, HER2-positive, and TN/basal-like bre...

Additional file 3: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S1. Peptide spectral counts by best ranked UniProt ID for 118 human breast tissues. (XLSX 768...

Additional file 2: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Figure S1. Processing of proteome data. Figure S2. Overlap in identified proteins between our study ...

Additional file 1: Table S1. of Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples

Sofia Waldemarson (1287219)
Emila Kurbasic (3417746)
Morten Krogh (26886)
Paolo Cifani (1575613)
Tord BerggĂĽrd (3417749)
Ăke Borg (3417743)
Peter James (348853)

June 2016

The clinical parameters of the tumors used in the 2D-DIGE analysis are given in this table: Sex, tum...

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang
Ming Zhou
Tiffany H. Dorsey
DaRue A. Prieto
Xin W. Wang
Eytan Ruppin
Timothy D. Veenstra
Stefan Ambs

December 2018

Abstract Background Transcriptome analysis of breast cancer discovered distinct disease subtypes of ...

Integrated Proteotranscriptomics of Breast Cancer Reveals Globally Increased Protein-mRNA Concordance Associated with Subtypes and Survival

Tang, Wei
Zhou, Ming
Dorsey, Tiffany H
Prieto, DaRue A
Wang, Xin W
Ruppin, Eytan
Veenstra, Timothy
Ambs, Stefan

December 2018

BACKGROUND: Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical...

Integrated Proteotranscriptomics of Breast Cancer Reveals Globally Increased Protein-mRNA Concordance Associated with Subtypes and Survival

Tang, Wei
Zhou, Ming
Dorsey, Tiffany H
Prieto, DaRue A
Wang, Xin W
Ruppin, Eytan
Veenstra, Timothy
Ambs, Stefan

December 2018

BACKGROUND: Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical...

Additional file 8 of An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping

Gayathri Thillaiyampalam (4711104)
Fabio Liberante (4711101)
Liam Murray (584595)
Chris Cardwell (4676743)
Ken Mills (204775)
Shu-Dong Zhang (231229)

December 2017

Tumor vs Normal 5 sub-gene signatures. The 5 non-joint 83-gene signatures are included, each consist...

Additional file 2: Table S7. of Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer

Guanglong Jiang (3469451)
Shijun Zhang (123373)
Aida Yazdanparast (3469457)
Meng Li (79487)
Aniruddha Pawar (3469454)
Yunlong Liu (46477)
Sai Inavolu (3469448)
Lijun Cheng (3469445)

August 2016

Correlation coefficient r across 4 genomics level comparison in breast cancer. (XLSX 1527 kb

Additional file 5 of An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping

Gayathri Thillaiyampalam (4711104)
Fabio Liberante (4711101)
Liam Murray (584595)
Chris Cardwell (4676743)
Ken Mills (204775)
Shu-Dong Zhang (231229)

December 2017

Tumor vs Adjacent differentially expressed genes. The full list of 164 significant genes selected fr...

Additional file 9: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S7. Proteins (nâ=â285) whose abundance in breast tumors correlated with tumor grade. (XLS...

Additional file 7: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S5. Significantly differentially expressed proteins between breast tumors and adjacent non-ca...

Additional file 12: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S10. Concordance values (rho) for 5677 protein-mRNA pairs in breast tumors (nâ=â59). (XLS...

Additional file 10: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S8. Proliferation score and global protein-mRNA concordance values for 59 breast tumors. (XLS...

Additional file 4: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S2. Enrichment of differently expressed protein-coding genes in KEGG pathways (tumor vs. adja...

Additional file 6: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S4. Most differentially expressed proteins between LumA, HER2-positive, and TN/basal-like bre...

Additional file 3: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S1. Peptide spectral counts by best ranked UniProt ID for 118 human breast tissues. (XLSX 768...

Additional file 2: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Figure S1. Processing of proteome data. Figure S2. Overlap in identified proteins between our study ...

Additional file 1: Table S1. of Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples

Sofia Waldemarson (1287219)
Emila Kurbasic (3417746)
Morten Krogh (26886)
Paolo Cifani (1575613)
Tord BerggĂĽrd (3417749)
Ăke Borg (3417743)
Peter James (348853)

June 2016

The clinical parameters of the tumors used in the 2D-DIGE analysis are given in this table: Sex, tum...

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang
Ming Zhou
Tiffany H. Dorsey
DaRue A. Prieto
Xin W. Wang
Eytan Ruppin
Timothy D. Veenstra
Stefan Ambs

December 2018

Abstract Background Transcriptome analysis of breast cancer discovered distinct disease subtypes of ...

Integrated Proteotranscriptomics of Breast Cancer Reveals Globally Increased Protein-mRNA Concordance Associated with Subtypes and Survival

Tang, Wei
Zhou, Ming
Dorsey, Tiffany H
Prieto, DaRue A
Wang, Xin W
Ruppin, Eytan
Veenstra, Timothy
Ambs, Stefan

December 2018

BACKGROUND: Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical...

Integrated Proteotranscriptomics of Breast Cancer Reveals Globally Increased Protein-mRNA Concordance Associated with Subtypes and Survival

Tang, Wei
Zhou, Ming
Dorsey, Tiffany H
Prieto, DaRue A
Wang, Xin W
Ruppin, Eytan
Veenstra, Timothy
Ambs, Stefan

December 2018

BACKGROUND: Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical...

Additional file 8 of An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping

Gayathri Thillaiyampalam (4711104)
Fabio Liberante (4711101)
Liam Murray (584595)
Chris Cardwell (4676743)
Ken Mills (204775)
Shu-Dong Zhang (231229)

December 2017

Tumor vs Normal 5 sub-gene signatures. The 5 non-joint 83-gene signatures are included, each consist...

Additional file 2: Table S7. of Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer

Guanglong Jiang (3469451)
Shijun Zhang (123373)
Aida Yazdanparast (3469457)
Meng Li (79487)
Aniruddha Pawar (3469454)
Yunlong Liu (46477)
Sai Inavolu (3469448)
Lijun Cheng (3469445)

August 2016

Correlation coefficient r across 4 genomics level comparison in breast cancer. (XLSX 1527 kb

Additional file 5 of An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping

Gayathri Thillaiyampalam (4711104)
Fabio Liberante (4711101)
Liam Murray (584595)
Chris Cardwell (4676743)
Ken Mills (204775)
Shu-Dong Zhang (231229)

December 2017

Tumor vs Adjacent differentially expressed genes. The full list of 164 significant genes selected fr...

Additional file 8: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Abstract

Extracted data

Additional file 8: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Abstract

Extracted data

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