Hermaphrodite and Male developmental datasets
The website provides a user-friendly platform for researchers and interested individuals to easily access and explore comprehensive gene expression atlas that covers both sexes of the nematode species, Caenorhabditis elegans, across all stages of development. In order to achieve this, the website has included RNA-seq profiles for five separate developmental stages, which are L1, L2, L3, L4, and YA for both sexes (Haque, R. et al. Nature Communications (2024)).
The gene expression data that has been generated is available for exploration by the community. Users can input the name of a gene/s and then browse through their corresponding gene expression profiles across all developmental stages in both sexes. These profiles can be visualized using individual line graphs that showcase the expression levels of the selected genes over developmental stage. Additionally, Bubble plot representations are also provided for any genes that exhibit differential expression in any of the five developmental stages of the two sexes. Bubble size represents log2 of fold change in expression of that gene (only genes that passed the filter p-adj = 0.05, |log2 fold change| >= 1 and basemean >= 5 are plotted), bubble color (cyan: males and orange: hermaphrodites) represents enrichment in either sex.
For instance, users can explore the expression atlas for the glr-5 and glr-6 genes in both sexes of C. elegans across all developmental stages, which can be achieved through the website’s easy-to-use interface.
Furthermore, users can compare the expression level of gene/s between two stages of the same sex and obtain output in the form of bar graphs. A positive value/bar graph signifies upregulation in the former group. For instance, a log2FoldChange of 2 in the comparison between L1 Male-L2 Male stage indicates a 2 log2FoldChange increase in expression in L1 Male. Conversely, a negative value/bar graph of -2 represents a 2 log2Fold Change increase in expression in L2 Male.