A database of Caenorhabditis elegans behavioral phenotypes

Journal name:
Nature Methods
Volume:
10,
Pages:
877–879
Year published:
DOI:
doi:10.1038/nmeth.2560
Received
Accepted
Published online

Using low-cost automated tracking microscopes, we have generated a behavioral database for 305 Caenorhabditis elegans strains, including 76 mutants with no previously described phenotype. The growing database currently consists of 9,203 short videos segmented to extract behavior and morphology features, and these videos and feature data are available online for further analysis. The database also includes summary statistics for 702 measures with statistical comparisons to wild-type controls so that phenotypes can be identified and understood by users.

At a glance

Figures

  1. The Worm Tracker 2.0 (WT2) system and phenomic database (http://wormbehavior.mrc-lmb.cam.ac.uk/).
    Figure 1: The Worm Tracker 2.0 (WT2) system and phenomic database (http://wormbehavior.mrc-lmb.cam.ac.uk/).

    (a) Schematic of the tracking hardware. (b) Videos are segmented to extract the worm contour and skeleton for phenotypic analysis. Frames from which contour and skeleton cannot be extracted are annotated with a color-coded border. The border indicates whether the frame was dropped (because of the processor's inability to keep up with incoming video frames), a stage movement occurred (blurring the worm image) or worm extraction failed (owing to an unrecognized shape); features are not computed from such frames. Numbers indicate the percentage of frames in each category. (c) Single-worm behavioral time series measuring maximum amplitude, defined relative to the major axis of the best-fit ellipse (Online Methods). Several shapes are shown with their corresponding amplitudes. (d) Single-worm path (same worm as in c). (e) Feature histogram measuring maximum amplitude (for the strain presented in c and d).

  2. Phenotypic summaries using selected features for subsets of strains.
    Figure 2: Phenotypic summaries using selected features for subsets of strains.

    Colors in the heat maps are used to indicate the q value for each feature for the comparison between each of the mutant strains listed on the right and the N2 reference data. Red values indicate features that have a significantly higher value in the mutant, whereas blue indicates significantly lower values in the mutant. Genes and features were both hierarchically clustered for easier comparison. (a) Subset of mutant strains with previously known locomotion phenotypes. (b) Subset of mutant strains with no previously reported locomotion phenotype. Abs, absolute; max, maximum.

References

  1. Ramani, A.K. et al. Cell 148, 792802 (2012).
  2. Houle, D., Govindaraju, D.R. & Omholt, S. Nat. Rev. Genet. 11, 855866 (2010).
  3. Husson, S.J., Costa, W.S., Schmitt, C. & Gottschalk, A. in WormBook (ed. Hobert, O.), doi:10.1895/wormbook.1.156.1 (2012).
  4. Hart, A.C. in WormBook (ed. Ambros, V.), doi:10.1895/wormbook.1.87.1 (2006).
  5. Geng, W., Cosman, P., Berry, C.C., Feng, Z. & Schafer, W.R. IEEE Trans. Biomed. Eng. 51, 18111820 (2004).
  6. Cronin, C.J. et al. BMC Genet. 6, 5 (2005).
  7. Huang, K.M., Cosman, P. & Schafer, W.R. J. Neurosci. Methods 171, 153164 (2008).
  8. Stephens, G.J., Johnson-Kerner, B., Bialek, W. & Ryu, W.S. PLOS Comput. Biol. 4, e1000028 (2008).
  9. Huang, K.M., Cosman, P. & Schafer, W.R. J. Neurosci. Methods 158, 323336 (2006).
  10. Storey, J.D. J. R. Stat. Soc. Series B Stat. Methodol. 64, 479498 (2002).
  11. Starich, T.A., Xu, J., Skerrett, I.M., Nicholson, B.J. & Shaw, J.E. Neural Dev. 4, 16 (2009).
  12. Yeh, E. et al. PLoS Biol. 6, e55 (2008).
  13. Boulin, T. et al. Proc. Natl. Acad. Sci. USA 105, 1859018595 (2008).
  14. Kindt, K.S. et al. Nat. Neurosci. 10, 568577 (2007).
  15. Jose, A.M., Bany, I.A., Chase, D.L. & Koelle, M.R. Genetics 175, 93105 (2007).
  16. Feng, Z. et al. Cell 127, 621633 (2006).
  17. Ghosh, R., Mohammadi, A., Kruglyak, L. & Ryu, W.S. BMC Biol. 10, 85 (2012).
  18. Brown, A.E., Yemini, E.I., Grundy, L.J., Jucikas, T. & Schafer, W.R. Proc. Natl. Acad. Sci. USA 110, 791796 (2013).
  19. Yemini, E., Kerr, R.A. & Schafer, W.R. Cold Spring Harb. Protoc. 2011, 14751479 (2011).
  20. Tsai, C.A. & Chen, J.J. Bioinformatics 25, 897903 (2009).
  21. Zhao, B., Khare, P., Feldman, L. & Dent, J.A. J. Neurosci. 23, 53195328 (2003).
  22. McGrath, P.T. et al. Neuron 61, 692699 (2009).
  23. Weber, K.P. et al. PLoS ONE 5, e13922 (2010).
  24. Brenner, S. Genetics 77, 7194 (1974).
  25. Otsu, N. IEEE Trans. Syst. Man. Cyber. 9, 6266 (1979).
  26. Freeman, H. IRE Trans. Electron. Comput. EC-10, 260268 (1961).
  27. Sulston, J.E. & Horvitz, H.R. Dev. Biol. 56, 110156 (1977).
  28. White, J.G., Southgate, E., Thomson, J.N. & Brenner, S. Philos. Trans. R. Soc. Lond. B Biol. Sci. 314, 1340 (1986).
  29. Alkema, M.J., Hunter-Ensor, M., Ringstad, N. & Horvitz, H.R. Neuron 46, 247260 (2005).

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Author information

Affiliations

  1. Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.

    • Eviatar Yemini,
    • Tadas Jucikas,
    • Laura J Grundy,
    • André E X Brown &
    • William R Schafer

Contributions

E.Y. created the WT2 system (hardware and software), analyzed data and wrote the paper. T.J. developed the WT2 analysis pipeline and built the online database. L.J.G. conducted all experiments. A.E.X.B. analyzed data, supervised research and wrote the paper. W.R.S. designed experiments, supervised research and wrote the paper.

Competing financial interests

The authors declare no competing financial interests.

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Supplementary information

PDF files

  1. Supplementary Text and Figures (2 MB)

    Supplementary Figures 1–6 and Supplementary Note

Excel files

  1. Supplementary Table 1 (19 KB)

    Supplementary Data Set

  2. Supplementary Table 2 (45 KB)

    Supplementary Data Set

  3. Supplementary Table 3 (48 KB)

    Supplementary Data Set

  4. Supplementary Table 4 (42 KB)

    Supplementary Data Set

  5. Supplementary Table 5 (7 MB)

    Supplementary Data Set

Additional data