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

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 1: of Expression of cancer-associated fibroblast related proteins in metastatic breast cancer: an immunohistochemical analysis

Hye Kim (3437315)
Woo Jung (3510701)
Ja Koo (3455753)

July 2015

Table S1. Source, clone, and dilution of the antibodies used. Table S2. Basal clinicopathologic char...

Additional file 1: of Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer

Yew Tang (4996598)
Szu-Chi Ho (4996595)
Elisabeth Tan (4996589)
Alvin Ng (270121)
John McPherson (545720)
Germaine Goh (798727)
Bin Teh (3548891)
Frederic Bard (798730)
Steven Rozen (4996592)

March 2018

Table S1. Growth media for breast cancer cell lines used in study. Table S2. PTEN protein abundance ...

Additional file 8: 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 S6. Concordance between protein-mRNA pairs in breast tumors and adjacent non-cancerous tissue...

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 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 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 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 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 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...

Additional file 10: Table S8. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

Significantly differentially expressed genes associated with the ratio of PRICKLE1 uc010skw.1 and uc...

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 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 1: of Expression of cancer-associated fibroblast related proteins in metastatic breast cancer: an immunohistochemical analysis

Hye Kim (3437315)
Woo Jung (3510701)
Ja Koo (3455753)

July 2015

Table S1. Source, clone, and dilution of the antibodies used. Table S2. Basal clinicopathologic char...

Additional file 1: of Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer

Yew Tang (4996598)
Szu-Chi Ho (4996595)
Elisabeth Tan (4996589)
Alvin Ng (270121)
John McPherson (545720)
Germaine Goh (798727)
Bin Teh (3548891)
Frederic Bard (798730)
Steven Rozen (4996592)

March 2018

Table S1. Growth media for breast cancer cell lines used in study. Table S2. PTEN protein abundance ...

Additional file 8: 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 S6. Concordance between protein-mRNA pairs in breast tumors and adjacent non-cancerous tissue...

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 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 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 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 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 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...

Additional file 10: Table S8. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

Significantly differentially expressed genes associated with the ratio of PRICKLE1 uc010skw.1 and uc...

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 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 1: of Expression of cancer-associated fibroblast related proteins in metastatic breast cancer: an immunohistochemical analysis

Hye Kim (3437315)
Woo Jung (3510701)
Ja Koo (3455753)

July 2015

Table S1. Source, clone, and dilution of the antibodies used. Table S2. Basal clinicopathologic char...

Additional file 1: of Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer

Yew Tang (4996598)
Szu-Chi Ho (4996595)
Elisabeth Tan (4996589)
Alvin Ng (270121)
John McPherson (545720)
Germaine Goh (798727)
Bin Teh (3548891)
Frederic Bard (798730)
Steven Rozen (4996592)

March 2018

Table S1. Growth media for breast cancer cell lines used in study. Table S2. PTEN protein abundance ...

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

Abstract

Extracted data

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

Abstract

Extracted data

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