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

About

About

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, which plots genes by their average expression level (x-axis), and by the extent to which transcripts are enriched in one of two samples being compared (y-axis). The user can select which two samples they wish to compare by clicking on cells or whole embryos above and below the plot.

Once the MA plot shows a comparison of interest, the user can filter results by significance of differential expression (via the P-value slider to the right). The user 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. The user can add any of these genes to a "watched gene list", which will keep those genes highlighted in subsequent MA plots. The user can also select large swaths of genes by dragging the mouse over a section of the MA plot. The user can prune genes out of the watched gene list by selecting them and then hitting the "remove selected" button.

The user can sort the watched gene list by a number of features (enrichment in on sample or the other, average abundance, and others), as well as export it. To view a summary of gene expression in all samples through all time points, the user can click on any gene name in the table, and retrieve a pictogram of all stages, with cells colored by quantitative expression data.

Attribution

Designed by Sophia Tintori and Patrick Golden

Coded by Patrick Golden
Source

Contact:
sophia.tintori@gmail.com, ptgolden@email.unc.edu

Please cite this tool as:
Tintori, S.C., Osborne Nishimura, E., Golden, P.T., Lieb, J.D., Goldstein, B. (2016). A transcriptional lineage of early C. elegans development. Developmental Cell 38(4), 430-444.

A Demonstration Video