An Automatic Cell Lineage Analyzer for C. elegans


The C. elegans cell lineage provides a unique opportunity to look at how cell lineage affects patterns of gene expression. We developed an automatic cell lineage analyzer that converts high-resolution images of worms into a data table showing fluorescence expression with single cell resolution. We generated expression profiles of 93 genes in 363 specific cells from L1 stage larvae and found that cells with identical fates can be formed by different gene regulatory pathways. Molecular signatures identified repeating cell fate modules within the cell lineage and enabled the generation of a molecular differentiation map that reveals points in the cell lineage when developmental fates of daughter cells begin to diverge. These results demonstrate insights that become possible using computational approaches to analyze quantitative expression from many genes in parallel using a digital gene expression atlas.

Guide to annotation


Liu, X., Long, F., Peng. H., Aerni, S., Jiang, M., Sanchez-Blanco, A., Murray, J., Waterston, R., Batzoglou, S., Myers, E. (2009) Analysis of gene regulation and cell fate from single-cell gene expression profiles in C. elegans. Cell 139, 622-633.

Long, F., Peng, H., Liu, X., Kim, S. K., Myers, E. (2009) A 3D digital atlas of C. elegans and its application to single-cell expression analysis. (2009) Nature Methods 6. 667-672.

Long, F., Peng, H., Liu, X., Kim, S.K., and Myers, G. (2008). Automatic Recognition of Cells (ARC) for 3D images of C. elegans. Recomb.

Peng, H., Long, F., Liu, X., Kim, S.K., and Myers, E.W. (2008). Straightening Caenorhabditis elegans images. Bioinformatics (Oxford, England) 24, 234-242