GeNets: a unified web platform for network-based genomic analyses

Taibo Li; April Kim; Joseph Rosenbluh; Heiko Horn; Liraz Greenfeld; David An; Andrew Zimmer; Arthur Liberzon; Jon Bistline; Ted Natoli; Yang Li; Aviad Tsherniak; Rajiv Narayan; Aravind Subramanian; Ted Liefeld; Bang Wong; Dawn Thompson; Sarah Calvo; Steve Carr; Jesse Boehm; Jake Jaffe; Jill Mesirov; Nir Hacohen; Aviv Regev; Kasper Lage

doi:10.1038/s41592-018-0039-6

GeNets: a unified web platform for network-based genomic analyses

Taibo Li, April Kim, Joseph Rosenbluh, Heiko Horn, Liraz Greenfeld, David An, Andrew Zimmer, Arthur Liberzon, Jon Bistline, Ted Natoli, Yang Li, Aviad Tsherniak, Rajiv Narayan, Aravind Subramanian, Ted Liefeld, Bang Wong, Dawn Thompson, Sarah Calvo, Steve Carr, Jesse BoehmJake Jaffe, Jill Mesirov, Nir Hacohen, Aviv Regev, Kasper Lage

Research output: Contribution to journal › Article › Research › peer-review

41 Citations (Scopus)

Abstract

Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.

Original language	English
Pages (from-to)	543-546
Number of pages	4
Journal	Nature Methods
Volume	15
DOIs	https://doi.org/10.1038/s41592-018-0039-6
Publication status	Published - Jul 2018
Externally published	Yes

Keywords

functional genomics
genetics research
network topology
systems biology

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10.1038/s41592-018-0039-6

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Li, T., Kim, A., Rosenbluh, J., Horn, H., Greenfeld, L., An, D., Zimmer, A., Liberzon, A., Bistline, J., Natoli, T., Li, Y., Tsherniak, A., Narayan, R., Subramanian, A., Liefeld, T., Wong, B., Thompson, D., Calvo, S., Carr, S., ... Lage, K. (2018). GeNets: a unified web platform for network-based genomic analyses. Nature Methods, 15, 543-546. https://doi.org/10.1038/s41592-018-0039-6

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title = "GeNets: a unified web platform for network-based genomic analyses",

abstract = "Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.",

keywords = "functional genomics, genetics research, network topology, systems biology",

author = "Taibo Li and April Kim and Joseph Rosenbluh and Heiko Horn and Liraz Greenfeld and David An and Andrew Zimmer and Arthur Liberzon and Jon Bistline and Ted Natoli and Yang Li and Aviad Tsherniak and Rajiv Narayan and Aravind Subramanian and Ted Liefeld and Bang Wong and Dawn Thompson and Sarah Calvo and Steve Carr and Jesse Boehm and Jake Jaffe and Jill Mesirov and Nir Hacohen and Aviv Regev and Kasper Lage",

year = "2018",

month = jul,

doi = "10.1038/s41592-018-0039-6",

language = "English",

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Li, T, Kim, A, Rosenbluh, J, Horn, H, Greenfeld, L, An, D, Zimmer, A, Liberzon, A, Bistline, J, Natoli, T, Li, Y, Tsherniak, A, Narayan, R, Subramanian, A, Liefeld, T, Wong, B, Thompson, D, Calvo, S, Carr, S, Boehm, J, Jaffe, J, Mesirov, J, Hacohen, N, Regev, A & Lage, K 2018, 'GeNets: a unified web platform for network-based genomic analyses', Nature Methods, vol. 15, pp. 543-546. https://doi.org/10.1038/s41592-018-0039-6

TY - JOUR

T1 - GeNets

T2 - a unified web platform for network-based genomic analyses

AU - Li, Taibo

AU - Kim, April

AU - Rosenbluh, Joseph

AU - Horn, Heiko

AU - Greenfeld, Liraz

AU - An, David

AU - Zimmer, Andrew

AU - Liberzon, Arthur

AU - Bistline, Jon

AU - Natoli, Ted

AU - Li, Yang

AU - Tsherniak, Aviad

AU - Narayan, Rajiv

AU - Subramanian, Aravind

AU - Liefeld, Ted

AU - Wong, Bang

AU - Thompson, Dawn

AU - Calvo, Sarah

AU - Carr, Steve

AU - Boehm, Jesse

AU - Jaffe, Jake

AU - Mesirov, Jill

AU - Hacohen, Nir

AU - Regev, Aviv

AU - Lage, Kasper

PY - 2018/7

Y1 - 2018/7

N2 - Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.

AB - Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.

KW - functional genomics

KW - genetics research

KW - network topology

KW - systems biology

UR - http://www.scopus.com/inward/record.url?scp=85048683997&partnerID=8YFLogxK

U2 - 10.1038/s41592-018-0039-6

DO - 10.1038/s41592-018-0039-6

M3 - Article

AN - SCOPUS:85048683997

SN - 1548-7091

VL - 15

SP - 543

EP - 546

JO - Nature Methods

JF - Nature Methods

ER -

GeNets: a unified web platform for network-based genomic analyses

Abstract

Keywords

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