Biological interpretation of genome-wide association studies using predicted gene functions

Tune H. Pers; Juha M. Karjalainen; Yingleong Chan; Harm-Jan Westra; Andrew R. Wood; Jian Yang; Julian C. Lui; Sailaja Vedantam; Stefan Gustafsson; Tonu Esko; Tim Frayling; Elizabeth K. Speliotes; Michael Boehnke; Soumya Raychaudhuri; Rudolf S. N. Fehrmann; Joel N. Hirschhorn; Lude Franke; Genetic Invest ANthropometric Trai; Stela McLachlan; Harry Campbell; Jackie Price; Igor Rudan; Jim Wilson

doi:10.1038/ncomms6890

Biological interpretation of genome-wide association studies using predicted gene functions

Tune H. Pers^*, Juha M. Karjalainen, Yingleong Chan, Harm-Jan Westra, Andrew R. Wood, Jian Yang, Julian C. Lui, Sailaja Vedantam, Stefan Gustafsson, Tonu Esko, Tim Frayling, Elizabeth K. Speliotes, Michael Boehnke, Soumya Raychaudhuri, Rudolf S. N. Fehrmann, Joel N. Hirschhorn, Lude Franke, Genetic Invest ANthropometric Trai, Stela McLachlan (Member of Consortium), Harry Campbell (Member of Consortium)Jackie Price (Member of Consortium), Igor Rudan (Member of Consortium), Jim Wilson (Member of Consortium)

^*Corresponding author for this work

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

Abstract

The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.

Original language	English
Article number	5890
Number of pages	9
Journal	Nature Communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms6890
Publication status	Published - 19 Jan 2015

Keywords / Materials (for Non-textual outputs)

CANDIDATE GENES
DATA SETS
DISEASE
NETWORK
LOCI
IDENTIFICATION
ARCHITECTURE
INTEGRATION
HEIGHT
COMMON

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10.1038/ncomms6890

Biological interpretation of genome-wide association studies using predicted gene functions
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Pers, T. H., Karjalainen, J. M., Chan, Y., Westra, H.-J., Wood, A. R., Yang, J., Lui, J. C., Vedantam, S., Gustafsson, S., Esko, T., Frayling, T., Speliotes, E. K., Boehnke, M., Raychaudhuri, S., Fehrmann, R. S. N., Hirschhorn, J. N., Franke, L., Genetic Invest ANthropometric Trai, McLachlan, S., ... Wilson, J. (2015). Biological interpretation of genome-wide association studies using predicted gene functions. Nature Communications, 6, Article 5890. https://doi.org/10.1038/ncomms6890

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title = "Biological interpretation of genome-wide association studies using predicted gene functions",

abstract = "The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.",

keywords = "CANDIDATE GENES, DATA SETS, DISEASE, NETWORK, LOCI, IDENTIFICATION, ARCHITECTURE, INTEGRATION, HEIGHT, COMMON",

author = "Pers, {Tune H.} and Karjalainen, {Juha M.} and Yingleong Chan and Harm-Jan Westra and Wood, {Andrew R.} and Jian Yang and Lui, {Julian C.} and Sailaja Vedantam and Stefan Gustafsson and Tonu Esko and Tim Frayling and Speliotes, {Elizabeth K.} and Michael Boehnke and Soumya Raychaudhuri and Fehrmann, {Rudolf S. N.} and Hirschhorn, {Joel N.} and Lude Franke and {Genetic Invest ANthropometric Trai} and Stela McLachlan and Harry Campbell and Jackie Price and Igor Rudan and Jim Wilson",

year = "2015",

month = jan,

day = "19",

doi = "10.1038/ncomms6890",

language = "English",

volume = "6",

journal = "Nature Communications",

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Pers, TH, Karjalainen, JM, Chan, Y, Westra, H-J, Wood, AR, Yang, J, Lui, JC, Vedantam, S, Gustafsson, S, Esko, T, Frayling, T, Speliotes, EK, Boehnke, M, Raychaudhuri, S, Fehrmann, RSN, Hirschhorn, JN, Franke, L, Genetic Invest ANthropometric Trai, McLachlan, S, Campbell, H , Price, J , Rudan, I & Wilson, J 2015, 'Biological interpretation of genome-wide association studies using predicted gene functions', Nature Communications, vol. 6, 5890. https://doi.org/10.1038/ncomms6890

TY - JOUR

T1 - Biological interpretation of genome-wide association studies using predicted gene functions

AU - Pers, Tune H.

AU - Karjalainen, Juha M.

AU - Chan, Yingleong

AU - Westra, Harm-Jan

AU - Wood, Andrew R.

AU - Yang, Jian

AU - Lui, Julian C.

AU - Vedantam, Sailaja

AU - Gustafsson, Stefan

AU - Esko, Tonu

AU - Frayling, Tim

AU - Speliotes, Elizabeth K.

AU - Boehnke, Michael

AU - Raychaudhuri, Soumya

AU - Fehrmann, Rudolf S. N.

AU - Hirschhorn, Joel N.

AU - Franke, Lude

AU - Genetic Invest ANthropometric Trai

A2 - McLachlan, Stela

A2 - Campbell, Harry

A2 - Price, Jackie

A2 - Rudan, Igor

A2 - Wilson, Jim

PY - 2015/1/19

Y1 - 2015/1/19

N2 - The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.

AB - The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.

KW - CANDIDATE GENES

KW - DATA SETS

KW - DISEASE

KW - NETWORK

KW - LOCI

KW - IDENTIFICATION

KW - ARCHITECTURE

KW - INTEGRATION

KW - HEIGHT

KW - COMMON

U2 - 10.1038/ncomms6890

DO - 10.1038/ncomms6890

M3 - Article

SN - 2041-1723

VL - 6

JO - Nature Communications

JF - Nature Communications

M1 - 5890

ER -

Biological interpretation of genome-wide association studies using predicted gene functions

Abstract

Keywords / Materials (for Non-textual outputs)

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