NetworkPainter: dynamic intracellular pathway animation in Cytobank

Jonathan R Karr; Harendra Guturu; Edward Y Chen; Stuart L Blair; Jonathan M Irish; Nikesh Kotecha; Markus W Covert

doi:10.1186/s12859-015-0602-4

NetworkPainter: dynamic intracellular pathway animation in Cytobank

BMC Bioinformatics. 2015 May 25:16:172. doi: 10.1186/s12859-015-0602-4.

Authors

Jonathan R Karr^{1

2}, Harendra Guturu³, Edward Y Chen⁴, Stuart L Blair⁵, Jonathan M Irish^{6

7

8

9}, Nikesh Kotecha^{10

11}, Markus W Covert¹²

Affiliations

¹ Graduate Program in Biophysics, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA. jkarr@stanfordalumni.org.
² Department of Genetics & Genomic Sciences, Mount Sinai School of Medicine, One Gustave L Levy Place, New York, NY, 10029, USA. jkarr@stanfordalumni.org.
³ Department of Electrical Engineering, Stanford University, 279 Campus Drive West, MC 5329, Stanford, CA, 94305, USA. hguturu@stanford.edu.
⁴ Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA. edchen@alumni.stanford.edu.
⁵ Cytobank Inc, 821 West El Camino Real, Mountain View, CA, 94040, USA. stu@cytobank.org.
⁶ Department of Medicine, Stanford University, 269 Campus Drive West, MC 5175, Stanford, CA, 94305, USA. jonathan.irish@vanderbilt.edu.
⁷ Department of Microbiology & Immunology, Stanford University, 269 Campus Drive West, MC 5175, Stanford, CA, 94305, USA. jonathan.irish@vanderbilt.edu.
⁸ Cytobank Inc, 821 West El Camino Real, Mountain View, CA, 94040, USA. jonathan.irish@vanderbilt.edu.
⁹ Department of Cancer Biology, Vanderbilt University, 740B Preston Building, 2220 Pierce Avenue, Nashville, TN, 37232, USA. jonathan.irish@vanderbilt.edu.
¹⁰ Graduate Program in Biomedical Informatics, Stanford University, 269 Campus Drive West, MC 5175, Stanford, CA, 94305, USA. nikesh@cytobank.org.
¹¹ Cytobank Inc, 821 West El Camino Real, Mountain View, CA, 94040, USA. nikesh@cytobank.org.
¹² Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA. mcovert@stanford.edu.

Abstract

Background: High-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data produced by these technologies is challenging. Visualization is needed to help researchers explore this data.

Results: We developed a web-based software program, NetworkPainter, to enable researchers to analyze dynamic cytometry data in the context of pathway diagrams. NetworkPainter provides researchers a graphical interface to draw and "paint" pathway diagrams with experimental data, producing animated diagrams which display the activity of each network node at each time point.

Conclusion: NetworkPainter enables researchers to more fully explore multi-parameter, dynamical cytometry data.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Computer Simulation
Cytoplasm / metabolism
Database Management Systems
Databases, Factual
Flow Cytometry / instrumentation*
Flow Cytometry / standards
Humans
Internet*
Leukocytes, Mononuclear / metabolism*
Signal Transduction*
Software*

Abstract

Publication types

MeSH terms

Grants and funding