Interactive visualizer of differential gene expression in the early C. elegans embryo



This is an interactive tool for comparing transcript abundance between each cell of the C. elegans embryo from the 1- to 16- cell stage.

At the center of the tool is an MA plot, in which genes are ploted by their average expression level (x-axis), and the extent to which transcripts are enriched in one of two samples being compared (y-axis). You can select two samples to compare by clicking on cells or whole embryos above and below the plot.

Once the MA plot shows your comparison of interest, you can filter results by significance of differential expression (via the P-value slider to the right). You can select specific genes by clicking on pixels within the MA plot. When each pixel is clicked, the gene(s) represented by that pixel will show up in the table on the right. You can add any of these genes to a "watched gene list", which will keep those genes highlighted in subsequent MA plots. You can also select large swaths of genes by dragging your mouse over a section of the MA plot.

Genes can be imported by name as well. In a text editor, create a file with each gene name on a separate line, and save it as a .csv. Click the "Import" button in the top right corner to load these genes into the table.

The watched gene list can be sorted by a number of features (enrichment in one sample or the other, average abundance, etc.), and can also be exported. To view a summary of gene expression in all samples through all time points, click on any gene name in the table. Underneath the table you will see a pictogram of all stages, with cells colored by quantitative expression data.


Designed by Sophia Tintori and Patrick Golden

Coded by Patrick Golden

Please cite this tool as:
Tintori, SC, Osborne Nishimura, E, Golden, PT, Lieb, JD, Goldstein, B. 2016. A Transcriptional Lineage of the Early C. elegans Embryo. Dev Cell. 2016 Aug 22;38(4):430-44. doi: 10.1016/j.devcel.2016.07.025.

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