Pathline: A tool for comparative functional genomics

M. Meyer, B. Wong, M. Styczynski, T. Munzner, H. Pfister

Research output: Contribution to journalArticle

Abstract

Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways, multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is the curvemap view, a depiction of time series data for comparison of gene activity and metabolite levels across multiple species. Pathline was developed in close collaboration with a team of genomic scientists. We validate our approach with case studies of the biologists' use of Pathline and report on how they use the tool to confirm existing findings and to discover new scientific insights.

Original languageEnglish (US)
Pages (from-to)1043-1052
Number of pages10
JournalComputer Graphics Forum
Volume29
Issue number3
DOIs
StatePublished - Jun 2010
Externally publishedYes

Fingerprint

Genes
Metabolites
Gene expression
Time series
Visualization
Genomics

Keywords

  • I.3.3 [Computer Graphics]: Picture/Image Generation - Line and curve generation

ASJC Scopus subject areas

  • Computer Networks and Communications

Cite this

Meyer, M., Wong, B., Styczynski, M., Munzner, T., & Pfister, H. (2010). Pathline: A tool for comparative functional genomics. Computer Graphics Forum, 29(3), 1043-1052. https://doi.org/10.1111/j.1467-8659.2009.01710.x

Pathline : A tool for comparative functional genomics. / Meyer, M.; Wong, B.; Styczynski, M.; Munzner, T.; Pfister, H.

In: Computer Graphics Forum, Vol. 29, No. 3, 06.2010, p. 1043-1052.

Research output: Contribution to journalArticle

Meyer, M, Wong, B, Styczynski, M, Munzner, T & Pfister, H 2010, 'Pathline: A tool for comparative functional genomics', Computer Graphics Forum, vol. 29, no. 3, pp. 1043-1052. https://doi.org/10.1111/j.1467-8659.2009.01710.x
Meyer M, Wong B, Styczynski M, Munzner T, Pfister H. Pathline: A tool for comparative functional genomics. Computer Graphics Forum. 2010 Jun;29(3):1043-1052. https://doi.org/10.1111/j.1467-8659.2009.01710.x
Meyer, M. ; Wong, B. ; Styczynski, M. ; Munzner, T. ; Pfister, H. / Pathline : A tool for comparative functional genomics. In: Computer Graphics Forum. 2010 ; Vol. 29, No. 3. pp. 1043-1052.
@article{5e250499c00a40c9938d84171d388fd8,
title = "Pathline: A tool for comparative functional genomics",
abstract = "Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways, multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is the curvemap view, a depiction of time series data for comparison of gene activity and metabolite levels across multiple species. Pathline was developed in close collaboration with a team of genomic scientists. We validate our approach with case studies of the biologists' use of Pathline and report on how they use the tool to confirm existing findings and to discover new scientific insights.",
keywords = "I.3.3 [Computer Graphics]: Picture/Image Generation - Line and curve generation",
author = "M. Meyer and B. Wong and M. Styczynski and T. Munzner and H. Pfister",
year = "2010",
month = "6",
doi = "10.1111/j.1467-8659.2009.01710.x",
language = "English (US)",
volume = "29",
pages = "1043--1052",
journal = "Computer Graphics Forum",
issn = "0167-7055",
publisher = "Wiley-Blackwell",
number = "3",

}

TY - JOUR

T1 - Pathline

T2 - A tool for comparative functional genomics

AU - Meyer, M.

AU - Wong, B.

AU - Styczynski, M.

AU - Munzner, T.

AU - Pfister, H.

PY - 2010/6

Y1 - 2010/6

N2 - Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways, multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is the curvemap view, a depiction of time series data for comparison of gene activity and metabolite levels across multiple species. Pathline was developed in close collaboration with a team of genomic scientists. We validate our approach with case studies of the biologists' use of Pathline and report on how they use the tool to confirm existing findings and to discover new scientific insights.

AB - Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways, multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is the curvemap view, a depiction of time series data for comparison of gene activity and metabolite levels across multiple species. Pathline was developed in close collaboration with a team of genomic scientists. We validate our approach with case studies of the biologists' use of Pathline and report on how they use the tool to confirm existing findings and to discover new scientific insights.

KW - I.3.3 [Computer Graphics]: Picture/Image Generation - Line and curve generation

UR - http://www.scopus.com/inward/record.url?scp=77955754224&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77955754224&partnerID=8YFLogxK

U2 - 10.1111/j.1467-8659.2009.01710.x

DO - 10.1111/j.1467-8659.2009.01710.x

M3 - Article

AN - SCOPUS:77955754224

VL - 29

SP - 1043

EP - 1052

JO - Computer Graphics Forum

JF - Computer Graphics Forum

SN - 0167-7055

IS - 3

ER -