Pathway and network analysis of cancer genomes

Pau Creixell; Jüri Reimand; Syed Haider; Guanming Wu; Tatsuhiro Shibata; Miguel Vazquez; Ville Mustonen; Abel Gonzalez-Perez; John Pearson; Chris Sander; Benjamin J. Raphael; Debora S. Marks; B. F.Francis Ouellette; Alfonso Valencia; Gary D. Bader; Paul C. Boutros; Joshua M. Stuart; Rune Linding; Nuria Lopez-Bigas; Lincoln D. Stein

doi:10.1038/nmeth.3440

Pathway and network analysis of cancer genomes

Pau Creixell, Jüri Reimand, Syed Haider, Guanming Wu, Tatsuhiro Shibata, Miguel Vazquez, Ville Mustonen, Abel Gonzalez-Perez, John Pearson, Chris Sander, Benjamin J. Raphael, Debora S. Marks, B. F.Francis Ouellette, Alfonso Valencia, Gary D. Bader, Paul C. Boutros, Joshua M. Stuart, Rune Linding, Nuria Lopez-Bigas, Lincoln D. Stein

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

222 Scopus citations

Abstract

Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.

Original language	English (US)
Pages (from-to)	615-621
Number of pages	7
Journal	Nature Methods
Volume	12
Issue number	7
DOIs	https://doi.org/10.1038/nmeth.3440
State	Published - Jun 30 2015
Externally published	Yes

All Science Journal Classification (ASJC) codes

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.3440

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Creixell, P., Reimand, J., Haider, S., Wu, G., Shibata, T., Vazquez, M., Mustonen, V., Gonzalez-Perez, A., Pearson, J., Sander, C., Raphael, B. J., Marks, D. S., Ouellette, B. F. F., Valencia, A., Bader, G. D., Boutros, P. C., Stuart, J. M., Linding, R., Lopez-Bigas, N., & Stein, L. D. (2015). Pathway and network analysis of cancer genomes. Nature Methods, 12(7), 615-621. https://doi.org/10.1038/nmeth.3440

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title = "Pathway and network analysis of cancer genomes",

abstract = "Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.",

author = "Pau Creixell and J{\"u}ri Reimand and Syed Haider and Guanming Wu and Tatsuhiro Shibata and Miguel Vazquez and Ville Mustonen and Abel Gonzalez-Perez and John Pearson and Chris Sander and Raphael, {Benjamin J.} and Marks, {Debora S.} and Ouellette, {B. F.Francis} and Alfonso Valencia and Bader, {Gary D.} and Boutros, {Paul C.} and Stuart, {Joshua M.} and Rune Linding and Nuria Lopez-Bigas and Stein, {Lincoln D.}",

note = "Funding Information: We gratefully acknowledge the assistance of J. Jennings during preparation of this manuscript. J.M.S. acknowledges support from the US National Cancer Institute (R01-CA180778 and U24-CA143858), Stand Up To Cancer, the Prostate Cancer Foundation and the Movember Foundation. P.C. is currently funded by a Ludwig Fund Postdoctoral Fellowship. P.C.B. and L.D.S. were supported by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario. P.C.B. was also supported by a Terry Fox Research Institute New Investigator Award and a Canadian Institutes of Health Research New Investigator Award. L.D.S. and G.W. acknowledge support from the US National Institutes of Health (NIH) and National Human Genome Research Institute (P41 HG003751). G.D.B. is supported by NRNB (NIH, National Institute of General Medical Sciences grant number P41 GM103504). Publisher Copyright: {\textcopyright} 2015 Nature America, Inc. All rights reserved.",

year = "2015",

month = jun,

day = "30",

doi = "10.1038/nmeth.3440",

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Creixell, P, Reimand, J, Haider, S, Wu, G, Shibata, T, Vazquez, M, Mustonen, V, Gonzalez-Perez, A, Pearson, J, Sander, C, Raphael, BJ, Marks, DS, Ouellette, BFF, Valencia, A, Bader, GD, Boutros, PC, Stuart, JM, Linding, R, Lopez-Bigas, N & Stein, LD 2015, 'Pathway and network analysis of cancer genomes', Nature Methods, vol. 12, no. 7, pp. 615-621. https://doi.org/10.1038/nmeth.3440

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T1 - Pathway and network analysis of cancer genomes

AU - Creixell, Pau

AU - Reimand, Jüri

AU - Haider, Syed

AU - Wu, Guanming

AU - Shibata, Tatsuhiro

AU - Vazquez, Miguel

AU - Mustonen, Ville

AU - Gonzalez-Perez, Abel

AU - Pearson, John

AU - Sander, Chris

AU - Raphael, Benjamin J.

AU - Marks, Debora S.

AU - Ouellette, B. F.Francis

AU - Valencia, Alfonso

AU - Bader, Gary D.

AU - Boutros, Paul C.

AU - Stuart, Joshua M.

AU - Linding, Rune

AU - Lopez-Bigas, Nuria

AU - Stein, Lincoln D.

N1 - Funding Information: We gratefully acknowledge the assistance of J. Jennings during preparation of this manuscript. J.M.S. acknowledges support from the US National Cancer Institute (R01-CA180778 and U24-CA143858), Stand Up To Cancer, the Prostate Cancer Foundation and the Movember Foundation. P.C. is currently funded by a Ludwig Fund Postdoctoral Fellowship. P.C.B. and L.D.S. were supported by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario. P.C.B. was also supported by a Terry Fox Research Institute New Investigator Award and a Canadian Institutes of Health Research New Investigator Award. L.D.S. and G.W. acknowledge support from the US National Institutes of Health (NIH) and National Human Genome Research Institute (P41 HG003751). G.D.B. is supported by NRNB (NIH, National Institute of General Medical Sciences grant number P41 GM103504). Publisher Copyright: © 2015 Nature America, Inc. All rights reserved.

PY - 2015/6/30

Y1 - 2015/6/30

N2 - Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.

AB - Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.

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JO - Nature Methods

JF - Nature Methods

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Pathway and network analysis of cancer genomes

Abstract

All Science Journal Classification (ASJC) codes

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