The role of visualization and 3-D printing in biological data mining

Talia L. Weiss, Amanda Zieselman, Douglas P. Hill, Solomon G. Diamond, Li Shen, Andrew Saykin, Jason H. Moore, Disease Neuroimaging Initiative Alzheimer's Disease Neuroimaging Initiative

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Abstract Background: Biological data mining is a powerful tool that can provide a wealth of information about patterns of genetic and genomic biomarkers of health and disease. A potential disadvantage of data mining is volume and complexity of the results that can often be overwhelming. It is our working hypothesis that visualization methods can greatly enhance our ability to make sense of data mining results. More specifically, we propose that 3-D printing has an important role to play as a visualization technology in biological data mining. We provide here a brief review of 3-D printing along with a case study to illustrate how it might be used in a research setting. Results: We present as a case study a genetic interaction network associated with grey matter density, an endophenotype for late onset Alzheimer's disease, as a physical model constructed with a 3-D printer. The synergy or interaction effects of multiple genetic variants were represented through a color gradient of the physical connections between nodes. The digital gene-gene interaction network was then 3-D printed to generate a physical network model. Conclusions: The physical 3-D gene-gene interaction network provided an easily manipulated, intuitive and creative way to visualize the synergistic relationships between the genetic variants and grey matter density in patients with late onset Alzheimer's disease. We discuss the advantages and disadvantages of this novel method of biological data mining visualization.

Original languageEnglish (US)
Article number56
JournalBioData Mining
Volume8
Issue number1
DOIs
StatePublished - Aug 5 2015

Fingerprint

Data Mining
3D
Data mining
Printing
Visualization
Genes
Gene
Alzheimer's Disease
Gene Regulatory Networks
Physical Model
Alzheimer Disease
3D printers
Interaction
Endophenotypes
Aptitude
Interaction Effects
Synergy
Biomarkers
Network Model
Genomics

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Weiss, T. L., Zieselman, A., Hill, D. P., Diamond, S. G., Shen, L., Saykin, A., ... Alzheimer's Disease Neuroimaging Initiative, D. N. I. (2015). The role of visualization and 3-D printing in biological data mining. BioData Mining, 8(1), [56]. https://doi.org/10.1186/s13040-015-0056-2

The role of visualization and 3-D printing in biological data mining. / Weiss, Talia L.; Zieselman, Amanda; Hill, Douglas P.; Diamond, Solomon G.; Shen, Li; Saykin, Andrew; Moore, Jason H.; Alzheimer's Disease Neuroimaging Initiative, Disease Neuroimaging Initiative.

In: BioData Mining, Vol. 8, No. 1, 56, 05.08.2015.

Research output: Contribution to journalArticle

Weiss, TL, Zieselman, A, Hill, DP, Diamond, SG, Shen, L, Saykin, A, Moore, JH & Alzheimer's Disease Neuroimaging Initiative, DNI 2015, 'The role of visualization and 3-D printing in biological data mining', BioData Mining, vol. 8, no. 1, 56. https://doi.org/10.1186/s13040-015-0056-2
Weiss, Talia L. ; Zieselman, Amanda ; Hill, Douglas P. ; Diamond, Solomon G. ; Shen, Li ; Saykin, Andrew ; Moore, Jason H. ; Alzheimer's Disease Neuroimaging Initiative, Disease Neuroimaging Initiative. / The role of visualization and 3-D printing in biological data mining. In: BioData Mining. 2015 ; Vol. 8, No. 1.
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