Integrative pathway enrichment analysis of multivariate omics data

Research output: Contribution to journal › Journal article › Research › peer-review

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Integrative pathway enrichment analysis of multivariate omics data. / Paczkowska, Marta; Barenboim, Jonathan; Sintupisut, Nardnisa; Fox, Natalie S.; Zhu, Helen; Abd-Rabbo, Diala; Mee, Miles W.; Boutros, Paul C.; Abascal, Federico; Amin, Samirkumar B.; Bader, Gary D.; Beroukhim, Rameen; Bertl, Johanna; Boroevich, Keith A.; Brunak, Søren; Campbell, Peter J.; Carlevaro-Fita, Joana; Chakravarty, Dimple; Chan, Calvin Wing Yiu; Chen, Ken; Choi, Jung Kyoon; Deu-Pons, Jordi; Dhingra, Priyanka; Diamanti, Klev; Feuerbach, Lars; Fink, J. Lynn; Fonseca, Nuno A.; Frigola, Joan; Gambacorti-Passerini, Carlo; Garsed, Dale W.; Gerstein, Mark; Getz, Gad; Gonzalez-Perez, Abel; Guo, Qianyun; Gut, Ivo G.; Haan, David; Hamilton, Mark P.; Haradhvala, Nicholas J.; Harmanci, Arif O.; Helmy, Mohamed; Herrmann, Carl; Hess, Julian M.; Hobolth, Asger; Hodzic, Ermin; Hong, Chen; Hornshøj, Henrik; Nielsen, Morten Muhlig; Pedersen, Jakob Skou; Sidiropoulos, Nikos; Weischenfeldt, Joachim.

In: Nature Communications, Vol. 11, No. 1, 735, 05.02.2020.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Paczkowska, M, Barenboim, J, Sintupisut, N, Fox, NS, Zhu, H, Abd-Rabbo, D, Mee, MW, Boutros, PC, Abascal, F, Amin, SB, Bader, GD, Beroukhim, R, Bertl, J, Boroevich, KA, Brunak, S, Campbell, PJ, Carlevaro-Fita, J, Chakravarty, D, Chan, CWY, Chen, K, Choi, JK, Deu-Pons, J, Dhingra, P, Diamanti, K, Feuerbach, L, Fink, JL, Fonseca, NA, Frigola, J, Gambacorti-Passerini, C, Garsed, DW, Gerstein, M, Getz, G, Gonzalez-Perez, A, Guo, Q, Gut, IG, Haan, D, Hamilton, MP, Haradhvala, NJ, Harmanci, AO, Helmy, M, Herrmann, C, Hess, JM, Hobolth, A, Hodzic, E, Hong, C, Hornshøj, H, Nielsen, MM, Pedersen, JS, Sidiropoulos, N & Weischenfeldt, J 2020, 'Integrative pathway enrichment analysis of multivariate omics data', Nature Communications, vol. 11, no. 1, 735. https://doi.org/10.1038/s41467-019-13983-9

APA

Paczkowska, M., Barenboim, J., Sintupisut, N., Fox, N. S., Zhu, H., Abd-Rabbo, D., Mee, M. W., Boutros, P. C., Abascal, F., Amin, S. B., Bader, G. D., Beroukhim, R., Bertl, J., Boroevich, K. A., Brunak, S., Campbell, P. J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y., ... Weischenfeldt, J. (2020). Integrative pathway enrichment analysis of multivariate omics data. Nature Communications, 11(1), [735]. https://doi.org/10.1038/s41467-019-13983-9

Vancouver

Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D et al. Integrative pathway enrichment analysis of multivariate omics data. Nature Communications. 2020 Feb 5;11(1). 735. https://doi.org/10.1038/s41467-019-13983-9

Author

Paczkowska, Marta ; Barenboim, Jonathan ; Sintupisut, Nardnisa ; Fox, Natalie S. ; Zhu, Helen ; Abd-Rabbo, Diala ; Mee, Miles W. ; Boutros, Paul C. ; Abascal, Federico ; Amin, Samirkumar B. ; Bader, Gary D. ; Beroukhim, Rameen ; Bertl, Johanna ; Boroevich, Keith A. ; Brunak, Søren ; Campbell, Peter J. ; Carlevaro-Fita, Joana ; Chakravarty, Dimple ; Chan, Calvin Wing Yiu ; Chen, Ken ; Choi, Jung Kyoon ; Deu-Pons, Jordi ; Dhingra, Priyanka ; Diamanti, Klev ; Feuerbach, Lars ; Fink, J. Lynn ; Fonseca, Nuno A. ; Frigola, Joan ; Gambacorti-Passerini, Carlo ; Garsed, Dale W. ; Gerstein, Mark ; Getz, Gad ; Gonzalez-Perez, Abel ; Guo, Qianyun ; Gut, Ivo G. ; Haan, David ; Hamilton, Mark P. ; Haradhvala, Nicholas J. ; Harmanci, Arif O. ; Helmy, Mohamed ; Herrmann, Carl ; Hess, Julian M. ; Hobolth, Asger ; Hodzic, Ermin ; Hong, Chen ; Hornshøj, Henrik ; Nielsen, Morten Muhlig ; Pedersen, Jakob Skou ; Sidiropoulos, Nikos ; Weischenfeldt, Joachim. / Integrative pathway enrichment analysis of multivariate omics data. In: Nature Communications. 2020 ; Vol. 11, No. 1.

Bibtex

@article{c1492f11318d4a738606e670a13c3862,
title = "Integrative pathway enrichment analysis of multivariate omics data",
abstract = "Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.",
author = "Marta Paczkowska and Jonathan Barenboim and Nardnisa Sintupisut and Fox, {Natalie S.} and Helen Zhu and Diala Abd-Rabbo and Mee, {Miles W.} and Boutros, {Paul C.} and Federico Abascal and Amin, {Samirkumar B.} and Bader, {Gary D.} and Rameen Beroukhim and Johanna Bertl and Boroevich, {Keith A.} and S{\o}ren Brunak and Campbell, {Peter J.} and Joana Carlevaro-Fita and Dimple Chakravarty and Chan, {Calvin Wing Yiu} and Ken Chen and Choi, {Jung Kyoon} and Jordi Deu-Pons and Priyanka Dhingra and Klev Diamanti and Lars Feuerbach and Fink, {J. Lynn} and Fonseca, {Nuno A.} and Joan Frigola and Carlo Gambacorti-Passerini and Garsed, {Dale W.} and Mark Gerstein and Gad Getz and Abel Gonzalez-Perez and Qianyun Guo and Gut, {Ivo G.} and David Haan and Hamilton, {Mark P.} and Haradhvala, {Nicholas J.} and Harmanci, {Arif O.} and Mohamed Helmy and Carl Herrmann and Hess, {Julian M.} and Asger Hobolth and Ermin Hodzic and Chen Hong and Henrik Hornsh{\o}j and Nielsen, {Morten Muhlig} and Pedersen, {Jakob Skou} and Nikos Sidiropoulos and Joachim Weischenfeldt",
year = "2020",
month = feb,
day = "5",
doi = "10.1038/s41467-019-13983-9",
language = "English",
volume = "11",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "nature publishing group",
number = "1",

}

RIS

TY - JOUR

T1 - Integrative pathway enrichment analysis of multivariate omics data

AU - Paczkowska, Marta

AU - Barenboim, Jonathan

AU - Sintupisut, Nardnisa

AU - Fox, Natalie S.

AU - Zhu, Helen

AU - Abd-Rabbo, Diala

AU - Mee, Miles W.

AU - Boutros, Paul C.

AU - Abascal, Federico

AU - Amin, Samirkumar B.

AU - Bader, Gary D.

AU - Beroukhim, Rameen

AU - Bertl, Johanna

AU - Boroevich, Keith A.

AU - Brunak, Søren

AU - Campbell, Peter J.

AU - Carlevaro-Fita, Joana

AU - Chakravarty, Dimple

AU - Chan, Calvin Wing Yiu

AU - Chen, Ken

AU - Choi, Jung Kyoon

AU - Deu-Pons, Jordi

AU - Dhingra, Priyanka

AU - Diamanti, Klev

AU - Feuerbach, Lars

AU - Fink, J. Lynn

AU - Fonseca, Nuno A.

AU - Frigola, Joan

AU - Gambacorti-Passerini, Carlo

AU - Garsed, Dale W.

AU - Gerstein, Mark

AU - Getz, Gad

AU - Gonzalez-Perez, Abel

AU - Guo, Qianyun

AU - Gut, Ivo G.

AU - Haan, David

AU - Hamilton, Mark P.

AU - Haradhvala, Nicholas J.

AU - Harmanci, Arif O.

AU - Helmy, Mohamed

AU - Herrmann, Carl

AU - Hess, Julian M.

AU - Hobolth, Asger

AU - Hodzic, Ermin

AU - Hong, Chen

AU - Hornshøj, Henrik

AU - Nielsen, Morten Muhlig

AU - Pedersen, Jakob Skou

AU - Sidiropoulos, Nikos

AU - Weischenfeldt, Joachim

PY - 2020/2/5

Y1 - 2020/2/5

N2 - Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.

AB - Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.

U2 - 10.1038/s41467-019-13983-9

DO - 10.1038/s41467-019-13983-9

M3 - Journal article

C2 - 32024846

AN - SCOPUS:85079073313

VL - 11

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 735

ER -

ID: 236371446