Type in any gene and the locus around it wil be displayed. The kb range for the window shown can also be changed. In yellow all genes from the genome annotation (ensembl, dm6) are shown. In blue are all detected ATAC peaks shown. Their IDs deploy their annotation (enh = putative enhancer, prom= putative promoter, CDS = putative coding sequence)
The 5135 sequenced cells were clustered using a weighted-nearest neighbour approach based on RNA+ATAC. The 12 retrieved clusters are depicted in a color-coded UMAP on the left side. Choose the number of a cluster to see where the cells belonging to that cluster would fall on the embryo after reconstructing them in space. The red color on the embryo indicates the cells .The color intensities change according to the probabilities of the cell reconstruction. The embryo is oriented dorsal up-anterior left.
For this cluster the following marker genes and marker peaks were detected (Note: not all clusters have marker genes/peaks. A ROC-identification method was used, which means marker genes/peaks can also classify negativly):
[marker genes and peaks]
Each gene and each peak can be visualized as a feature plot the UMAP. Just chose the Gene or Peak an they will be displayed in red.
DVMuX is an online resource tool which offers an easy way to explore the gene expression and the chromatin accessibility of the stage 6 Drosophila embryo in a spatial manner. It is highly inspired by its first version: DVEX (Drosophila Virtual Expression eXplorer) and accompanied by the following preprint puplication: --- TBC-----
DVMuX is created by Miriam Faxel. ----TBC----- Contact the author for questions, or troubleshooting.
The coordinate system used for visualization of gene patterns in DVMuX comes from the BDTNP project, in which the 3D positions of 6,000 nuclei were registered.
The spatial reconstruction of the single cells was performed with NovoSpaRc.
-> virtual embryo: check out virtual gene expressions or virtual chromatin accessibilities in 2D or 3D
-> Explore: genes and detected ATAC-peaks are shown genome wide and their vGEX and vCA can be displayed.
-> enhancer prediction:
- June 2023: prototype goes online
- January 2024: enhancer prediction added