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; SW van der Laan

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, , SW van der Laan

Research output: Contribution to journal › Article › Academic › 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
Journal	Nature Communications [E]
Volume	6
DOIs	https://doi.org/10.1038/ncomms6890
Publication status	Published - 2015

Keywords

Genome-Wide Association Study
Software

Access to Document

10.1038/ncomms6890

ncomms6890Final published version, 633 KBLicence: Taverne

Cite this

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., & van der Laan, SW. (2015). Biological interpretation of genome-wide association studies using predicted gene functions. Nature Communications [E], 6, Article 5890. https://doi.org/10.1038/ncomms6890

@article{a935eec764314d88b8e27363700a8cac,

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 = "Genome-Wide Association Study, Software",

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 {van der Laan}, SW and FW Asselbergs",

year = "2015",

doi = "10.1038/ncomms6890",

language = "English",

volume = "6",

journal = "Nature Communications [E]",

issn = "2041-1723",

publisher = "Nature Publishing Group",

}

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 & van der Laan, SW 2015, 'Biological interpretation of genome-wide association studies using predicted gene functions', Nature Communications [E], 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 - van der Laan, SW

AU - Asselbergs, FW

PY - 2015

Y1 - 2015

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 - Genome-Wide Association Study

KW - Software

U2 - 10.1038/ncomms6890

DO - 10.1038/ncomms6890

M3 - Article

C2 - 25597830

SN - 2041-1723

VL - 6

JO - Nature Communications [E]

JF - Nature Communications [E]

M1 - 5890

ER -

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

Abstract

Keywords

Access to Document

Fingerprint

Cite this