The worm struct has the following subfields: The control struct contains the control stats in an identical format to the worm struct stats, but without the zScores. The info struct contains the experimental annotation. CAS Bend Count. et al. Biol. Included in this dataset are most canonical unc and egl mutants as well as representative knockouts from receptor, channel and neuropeptide gene families with likely roles in nervous system function. If the distances are not identical, the distance of the larger side is used in place of the zero-crossing distance of the smaller side in order to expand the small side and achieve a symmetric window, centered at the frame of interest. This ignores small bends at the tip of the head and tail. Briefly, 48 tangent angles are calculated along the skeleton and rotated to have a mean angle of zero. Husson, S.J., Costa, W.S., Schmitt, C. & Gottschalk, A. in WormBook (ed. The protocol is also available online: http://www.mrc-lmb.cam.ac.uk/wormtracker/webcontent/trackingProtocol.pdf. Coils. The head is controlled by the first four bodywall muscles, per quadrant -- approximately 1/6 the length of the worm28. Natl. And, three types of MAT files are provided to access the strain data and statistics as well as the skeleton, contour, and feature data for each individual experiment, per frame. The worms head-tip and/or head velocity vectors if neither the Foraging, Forward Velocity, nor Backward Velocity were found significant. The wavelength is 627nm to avoid exciting a short-wavelength avoidance response through the C. elegans LITE-1 receptor. All strains were significantly different from wild type at q 0.05, including those representing 76 genes with no previously characterized phenotype (Supplementary Tables 35). The database consists of 9,203 short videos segmented to extract behavior and morphology features that are available online for further analysis. Likewise, dorsal and ventral bending were measured over the entire body, and in specific regions such as the head, tail, and midbody. Furthermore, we include Shapiro-Wilk tests of data normality, per measure, in pNormal and correction for multiple testing, using their False-Discovery rate q-value replacements, in qNormal. Individual experiment files also contain a motion state mode with values distinguishing forward (1), backward (1), and paused (0) states, per frame. Open Access When multiple histograms are plotted together, the smallest common bin size is used to downsample all the histograms to the same bin width and centers. Freeman, H. IRE Trans. The first two MAT file types, individual experiments and strain collections, share a similar format. Jose, A.M., Bany, I.A., Chase, D.L. 9, 6266 (1979). The data is always represented as both a mean and stdDev (standard deviation). Because re-centering the worm causes an abrupt change in both the image background and the worms location, these changes are simply measured as the pixel variance in the difference between subsequent frames. This resulted in a mean of 63 controls, per strain collection, with a minimum of 18 and a standard deviation of 29. It is our hope that making these data available to the community will encourage other researchers to contribute collaboratively to the emerging science of behavioral informatics. These widths are converted to microns. Abstract. 11, 855866 (2010). Products. Our knowledge of the Caenorhabditis elegans genome has increased substantially since the publication of the 1988 C. elegans book (Emmons 1988); even the genome size has changed from an estimated 80 106 base pairs to 100 106 base pairs. This resulted in a mean of 24 worms per strain with a minimum of 12 and a standard deviation of 14. sharing sensitive information, make sure youre on a federal To ensure this was not an artifact of our methodology we chose a second method to verify our result. The worms are given 30 minutes to habituate, and are then tracked for 15 minutes. Turns. Worm pixels are segmented from the background using the Otsu method25 to find a threshold. The worms tail bend mean and/or standard deviation. USA 105, 1859018595 (2008). Worm Phenotype Ontology: Integrating phenotype data within - Springer The table of contents page also shows an overview with the experiment annotation and its phenotypic ontology (see the section titled Phenotypic Ontology). Moreover, on each plot, the locations for coiling events are marked by a + and those for omega turns are marked by an x. A database of C. elegans behavioral phenotypes - PMC The head is detected in each chunk of oriented frames. Worms were maintained on NGM (Nematode-Growth-Medium) agar plates seeded with E. coli strain OP50 as food, in a 20 degree incubator according to the standard method . We also analyzed LSJ1, a more distant relative of N2. Brown AE, Yemini EI, Grundy LJ, Jucikas T, Schafer WR. Stephens, G.J., Johnson-Kerner, B., Bialek, W. & Ryu, W.S. & Shaw, J.E. To close this phenotyping gap, it is desirable to have a system that is capable of measuring phenotypes both extensively and intensively2. An opal diffuser provides roughly uniform lighting over the FOV. The detail pages present a detailed view of the histograms for every feature. This project was funded by the MRC (MC-A022- 5PB91) the NIH/NIDA (DA018341), a Gates Cambridge Scholarship (to E.Y). Brenner S. The genetics of Caenorhabditis elegans. The direction is defined as the angle (between centroids) from the start to the end frame, relative to the worms overall body angle, divided by the time between both frames. They also include the full skeleton and the centroid of the contour, per frame, permitting novel feature computations. The authors declare no competing financial interests. We only include data collected Monday through Saturday, from 8am to 6pm. Publications. Journal of the royal statistical society: series B. Starich TA, Xu J, Skerrett IM, Nicholson BJ, Shaw JE. The head and tail centroids are computed as the mean of their respective skeleton points. PLoS ONE 5, e13922 (2010). We use a Fourier transform to measure the amplitude and frequency within the window described above. Digital development: a database of cell lineage differentiation in C A common notation is used to define the body parts (Supplementary Fig. The overall orientation is measured as the angular direction from the tail to the head centroid. With this in place, stage movement frames are discarded and each interval between stage movements is assigned a stage location. Red values indicate features that have a significantly higher value in the mutant while blue indicates significantly lower values. Cyber. Alkema, M.J., Hunter-Ensor, M., Ringstad, N. & Horvitz, H.R. This ontology uses a mixed-case prefix. The statistical values include: a) the number of worms providing measurements (WORMS); b) the number of measurements sampled for the collection of worms (SAMPLES); c) the mean of the data (ALL) alongside the SEM and, when the data is signed, the means for the absolute data values (ABS), positive data values only (POS), and negative data values only (NEG) alongside their SEMs as well; d) the p-value results using Wilcoxon rank-sum testing and q-value results using False Discovery Rate correction (for multiple tests across 329 strain collections by 702 feature measurements), both labeled accordingly (respectively p and q); e) event features also display their mean frequency (FREQ), the mean percentage of time spent in the event relative to the total experiment time (TIME), and, when available, the mean percentage of distance traveled during the event relative to the total distance covered during the experiment (DIST). Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. The criteria for backward motion is identical except the worm must be moving backwards (the midbody speed must be negatively signed). Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely . The database also includes summary statistics for 702 measures with . The database stores data from recent systematic studies of cell lineage differentiation in the C. elegans embryo containing ~200 conserved genes, 1400 perturbed cell lineages and 600 000 digitized single cells. Eigen Projections. The video frame annotations are presented for all frames with a reference specifying the annotations numerical id, the function it originated from, and a message describing the meaning of the annotation. Head Motion. Storey, J.D. The worms head bend mean and/or standard deviation. The worm is defined in a state of forward motion when a period, more than half a second long, is observed wherein: a) the worm travels at least 5% of its mean length over the entire period; and, b) the worms speed is at least 5% of its length, per second, in each frame. The database consists of 9,203 short videos segmented to extract behavior and morphology features that are available online for further analysis. Once again, every group was found to be significantly different from the wild type at q 0.05, bearing out the results of our primary methodology (Supplementary Table 3). Huang, K.M., Cosman, P. & Schafer, W.R. J. Neurosci. New videos maintain 30fps. These primary features were also evaluated in different contexts to give more complex parameterization; for example, mean speed was measured over the entire movie, as well as independently for periods when the animal was moving either forward or backward. If the worms location is still missing at either the start or end, the path curvature is marked unknown at this point. The angular speed is signed negatively whenever its vector points towards the worms ventral side. To assess the influence of these factors (hour, day, and month), one-way ANOVAs were performed with Bonferroni correction for 18 tests and checked for significance at p 0.05. et al. 51, 18111820 (2004). Rev. The worm bend mean angles (described in the section on Posture) show a roughly periodic signal as the crawling wave travels along the worms body. Proportion. In the early stage of the C. elegans sequencing project, the ab initio gene prediction program Genefinder was used to find protein-coding genes. 1b). An example histogram, at the beginning of the first summary page, provides a reference to interpret the aforementioned statistical measures. B Biol. Each group was assigned its minimum q-value as a measure of group significance.
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