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Exploring the Network of Essential C. elegans Genes Using N-Browse

The sterile collection analysis (554 genes; Green et al., 2011) and the time-lapse DIC filming of embryos (661 genes; Sönnichsen et al., 2005) together provide knockdown profiles for 885 essential C. elegans genes, 330 of which were profiled in both screens. We integrated these datasets into an in silico network that can be viewed at different levels of functional resolution using the CSI (Connection Specificity Index), a network context-based measure that ranks the significance of functional links between genes (Green et al., 2011). Functional modularity can be explored at different levels of resolution in the network by dialing up or down the CSI threshold used to display functional connections between genes. At high CSI thresholds, only genes with very similar knockdown phenotypes are connected; at lower CSI thresholds, genes whose knockdown phenotypes are more generally similar are also linked (Green et al., 2011). The dynamic graphical interface used to visualize the network is N-Browse, an interactive Java-based tool (Kao and Gunsalus, 2008). In N-Browse, the user can display the functional connections identified by the Sönnichsen et al. (2005) and Green et al. (2011) high-content screens using different CSI thresholds and can also display connections based on prior expression correlation and protein-protein interaction data sets.

Access to N-Browse is provided through the set of links below.

Video demonstrating how to use N-Browse
Written instructions describing how to use N-Browse
Connect to N-Browse
Download a preset view of the whole network (PC specific version - NOTE: this file is 35 MB)
Download a preset view of the whole network (Mac specific version - NOTE: this file is 40 MB)

References

Sönnichsen, B., Koski, L., Walsh, A., Marschall, P., Neumann, B., Brehm, M., Alleaume, A., Artelt, J., Bettencourt, P., Cassin, E., Hewitson, M., Holz, C., Khan, M., Lazik, S., Martin, C., Nitzsche, B., Ruer, M., Stamford, J., Winzi, M., Heinkel, R., Roder, M., Finell, J., Hantsch, H., Jones, S., Jones, M., Piano, F., Gunsalus, K., Oegema, K., Gönczy, P., Coulson, A., Hyman, A.A. and C.J. Echeverri. (2005). Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462-469. [PubMed]

Green, R., Kao, H.L., Audhya, A., Arur, S., Mayers, J., Fridolfsson, H., Schulman, M., Schloissnig, S., Niessen, S., Laband, K., Wang, S., Starr, D., Hyman, A.A., Desai, A., Schedl, T., Gunsalus, K. C., Piano, F., and Oegema, K. (2011). High-Resolution Phenotypic Profiling Based on the Architecture of a Complex Tissue. Submitted.

Kao, H.L., and Gunsalus, K.C. (2008). Browsing multidimensional molecular networks with the generic network browser (N-Browse). Curr. Protoc. Bioinform. 23:9.11.1-9.11.21. [PubMed]