A major challenge of the post-genomic era is to translate the parts lists, generated by genome sequencing, into functional maps of the interconnected pathways that execute diverse cellular processes. In animal cells, high-content screening has emerged as the method of choice for profiling gene function. In a high-content screen, light microscopy is used to assess the phenotype resulting from inhibition of individual genes, typically by RNA-mediated interference.

Phenobank provides access to the primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. This set of 900 genes represents the majority of non-redundant genes essential for basic conserved processes common to all cells.

In the first high-content screen, the set of genes required for embryonic viability was screened by timelapse Differential Interference Contrast (DIC) filming of the first two embryonic divisions (Sönnichsen et al., 2005). This screen identified 661 genes that gave a detectable DIC phenotype and placed these genes into 26 phenotypic classes. In the second high-content screen the set of genes required for embryo production was screened using two-color fluorescence confocal microscopy to image the syncytial gonad, a complex tissue whose architecture depends on a spectrum of interacting cellular processes (Green et al., 2011). This screen placed the 554 genes in the sterile collection into 102 phenotypic classes. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens. Written instructions and a video demonstrating how to search Phenobank can be accessed by clicking on the links below.

Phenotypic profiles can be similar, very similar, or essentially identical-reflecting increasingly close functional connections between genes. To visualize functional modularity at different levels of resolution, we integrated to the two high-content datasets in N-Browse, an interactive Java-based tool that provides a graphical interface for displaying gene networks (Kao and Gunsalus, 2008). The datasets were integrated using the CSI (Connection Specificity Index), a network context-based measure that ranks the significance of functional links between genes (Green et al., 2011). 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 integrated network based on the embryo-filming and gonad morphology data consists of 818 gene nodes and 3382 high-significance connections (Green et al., 2011). Instructions for accessing the N-Browse network along with a demo video can be found in Phenobank under the N-Browse tab.

Video demonstrating how to search Phenobank
Written instructions for searching Phenobank

Gonczy P, Echeverri G, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlu N, Bork P, Hyman AA. (2000) Functional genomic analysis of cell division in C.elegans using RNAi of genes on chromosome III. Nature 408(6810): 331-336.
[PubMed]

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]