An information retrieval perspective on visualization of gene expression data with ontological annotation

Jaakko Peltonen; Helena Aidos; Nils Gehlenborg; Alvis Brazma; Samuel Kaski

doi:10.1109/ICASSP.2010.5495665

An information retrieval perspective on visualization of gene expression data with ontological annotation

Jaakko Peltonen, Helena Aidos, Nils Gehlenborg, Alvis Brazma, Samuel Kaski

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

Abstract

High-dimensional data are often visualized by dimensionality reduction methods whose goals are not directly related to visualization. We use a recent formalization of visualization as information retrieval and apply that formalism to data with structured annotations: we analyze gene expression data with annotations from the Gene Ontology (GO). We show that using the GO information in visualization yields better retrieval with respect to known ontological relationships and allows discovery of data properties not explained by the ontology.

Original language	English
Title of host publication	Proceedings of ICASSP 2010, 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing
Publisher	IEEE
Pages	2178-2181
ISBN (Print)	978-1-4244-4295-9
DOIs	https://doi.org/10.1109/ICASSP.2010.5495665
Publication status	Published - 2010
Externally published	Yes
Publication type	A4 Article in conference proceedings

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10.1109/ICASSP.2010.5495665

https://research.cs.aalto.fi/pml/papers/icassp10_preprint.pdf

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title = "An information retrieval perspective on visualization of gene expression data with ontological annotation",

abstract = "High-dimensional data are often visualized by dimensionality reduction methods whose goals are not directly related to visualization. We use a recent formalization of visualization as information retrieval and apply that formalism to data with structured annotations: we analyze gene expression data with annotations from the Gene Ontology (GO). We show that using the GO information in visualization yields better retrieval with respect to known ontological relationships and allows discovery of data properties not explained by the ontology.",

author = "Jaakko Peltonen and Helena Aidos and Nils Gehlenborg and Alvis Brazma and Samuel Kaski",

year = "2010",

doi = "10.1109/ICASSP.2010.5495665",

language = "English",

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booktitle = "Proceedings of ICASSP 2010, 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing",

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address = "United States",

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An information retrieval perspective on visualization of gene expression data with ontological annotation. / Peltonen, Jaakko; Aidos, Helena; Gehlenborg, Nils et al.
Proceedings of ICASSP 2010, 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing. IEEE, 2010. p. 2178-2181.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

TY - GEN

T1 - An information retrieval perspective on visualization of gene expression data with ontological annotation

AU - Peltonen, Jaakko

AU - Aidos, Helena

AU - Gehlenborg, Nils

AU - Brazma, Alvis

AU - Kaski, Samuel

PY - 2010

Y1 - 2010

N2 - High-dimensional data are often visualized by dimensionality reduction methods whose goals are not directly related to visualization. We use a recent formalization of visualization as information retrieval and apply that formalism to data with structured annotations: we analyze gene expression data with annotations from the Gene Ontology (GO). We show that using the GO information in visualization yields better retrieval with respect to known ontological relationships and allows discovery of data properties not explained by the ontology.

AB - High-dimensional data are often visualized by dimensionality reduction methods whose goals are not directly related to visualization. We use a recent formalization of visualization as information retrieval and apply that formalism to data with structured annotations: we analyze gene expression data with annotations from the Gene Ontology (GO). We show that using the GO information in visualization yields better retrieval with respect to known ontological relationships and allows discovery of data properties not explained by the ontology.

U2 - 10.1109/ICASSP.2010.5495665

DO - 10.1109/ICASSP.2010.5495665

M3 - Conference contribution

SN - 978-1-4244-4295-9

SP - 2178

EP - 2181

BT - Proceedings of ICASSP 2010, 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing

PB - IEEE

ER -

An information retrieval perspective on visualization of gene expression data with ontological annotation

Abstract

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