Abstract
Cytometry techniques allow to quantify morphological characteristics and protein abundances at a single-cell level. Data collected with these techniques can be used for addressing the fascinating, yet challenging problem of reconstructing the network of protein interactions forming signaling pathways and governing cell biological mechanisms. Network reconstruction is an established and well studied problem in the machine learning and data mining fields, with several algorithms already available. In this paper, we present the first web-oriented application, SCENERY, that allows scientists to rapidly apply state-of-the-art network-reconstruction methods on cytometry data. SCENERY comes with an easy-to-use user interface, a modular architecture, and advanced visualization functions. The functionalities of the application are illustrated on data from a publicly available immunology experiment.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ullrich, A., Schlessinger, J.: Signal transduction by receptors with tyrosine kinase activity. Cell 61(2), 203–212 (1990)
Bendall, S., Nolan, G., Roederer, M., Chattopadhyay, P.: A Deep Profilers Guide to Cytometry. Trends Immunol. 33(7), 323–332 (2012)
Marbach, D., Costello, J.C., Kffner, R., et. al.: Wisdom of crowds for robust gene network inference. Nat. Methods 9(8), 796–804 (2012)
Sachs, K., Perez, O., Pe’er, D., Lauffenburger, D.A., Nolan, G.P.: Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data. Science 308, 523–529 (2005)
Itani, S., Ohannessian, M., Sachs, K., et. al.: Structure learning in causal cyclic networks. In: JMLR Workshop and Conference Proceedings (2010)
Qiu, P., Simonds, E.F., Bendall, S.C., et. al.: Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat. Biotech. 29, 886–891 (2011)
Lagani, V., Triantafillou, S., Ball, B., Tegner, J., Tsamardinos, I.: Probabilistic Computational Causal Discovery for Systems Biology. A Computational Modeling Approach. In: Uncertainty in Biology (2015)
Bik, H.M., Goldstein, M.C.: An Introduction to Social Media for Scientists. PLoS Biol. 11(4), e1001535 (2013). doi:10.1371/journal.pbio.1001535
Kotecha, N., Krutzik, PO., Irish, JM.: Web-based Analysis and Publication of Flow Cytometry Experiments. Curr. Prot. Cyt., Chapter 10, Unit10.17. (2010)
Levine, J.H.., Simonds, E.F.., Bendall, S.C., et. al.: Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell (2015)
Kelkar, S. A.: Usability and Human-Computer Interaction: A Concise Study, p. 306 (2009)
Priem, J., Costello, K.L.: How and why scholars cite on Twitter. Proceedings of ASIST 47(1), 104 (2010)
Lagani, V., Athineou, G., Borboudakis, G. and Tsamardinos, I.: MXM: Discovering Multiple, Statistically-Equivalent Signatures. R package version 0.4.3. (2015). http://CRAN.R-project.org/package=MXM
Scutari, M.: Learning Bayesian Networks with the bnlearn R Package. JSS 35(3), 1–22 (2010). http://www.jstatsoft.org/v35/i03/
Kalisch, M., Maechler, M., Colombo, D., Maathuis, M.H., Buehlmann, P.: Causal Inference Using Graphical Models with the R Package pcalg. JSS 47(11), 1–26 (2012). http://www.jstatsoft.org/v47/i11/
Karampelas, P., Basdekis, I. and Stephanidis, C.: Web user interface design strategy: Designing for device independence. In: C. Stephanidis (ed.). Proceedings of the 13th International Conference on Human-Computer Interaction HCI International 2009, July 19-24, San Diego, CA, USA., pp. 515–524 (2009)
Bendall, S.C., Simonds, E.F., et al.: Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum. Science 332(6030), 687–696 (2011)
Dal Porto, J., Gauld, S., Merrell, et.al.: B cell antigen receptor signaling 101. Mol. Imm. 41, 599–613 (2004)
Ishiai, M., Kurosaki, M., Pappu, R., et al.: BLNK Required for Coupling Syk to PLCg2 and Rac1-JNK in B Cells. Imm. 10, 117–125 (1999)
Guinamard, R., Signoret, N., Ishiai, et al.: B cell antigen receptor engagement inhibits stromal cell-derived factor (SDF)-1alpha chemotaxis and promotes protein kinase C (PKC)-induced internalization of CXCR4. J. Exp. Med. 189(9), 1461–1466 (1999)
Cargnello, M., Roux, P.: Activation and Function of the MAPKs and Their Substrates, the MAPK-Activated Protein Kinases. Microbiol. Mol. Biol. Rev. 75(1), 5083 (2011)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this paper
Cite this paper
Athineou, G., Papoutsoglou, G., Triantafillou, S., Basdekis, I., Lagani, V., Tsamardinos, I. (2016). SCENERY: A Web-Based Application for Network Reconstruction and Visualization of Cytometry Data. In: Saberi Mohamad, M., Rocha, M., Fdez-Riverola, F., DomÃnguez Mayo, F., De Paz, J. (eds) 10th International Conference on Practical Applications of Computational Biology & Bioinformatics. PACBB 2016. Advances in Intelligent Systems and Computing, vol 477. Springer, Cham. https://doi.org/10.1007/978-3-319-40126-3_21
Download citation
DOI: https://doi.org/10.1007/978-3-319-40126-3_21
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-40125-6
Online ISBN: 978-3-319-40126-3
eBook Packages: EngineeringEngineering (R0)