This section allows the user to identify spatially similar genes. Given a gene and a threshold for its expression pattern, the epression patterns of a set of genes are then calculated and compared against the pattern of the selected gene. The returned table is sorted by maximum spatial expression similarity with the selected gene, as measured by the Manhattan distance.
Note: the computation is performed by default for the set of highly variable genes. Selecting all genes will result in a longer computation time.
Download
The following data is available for direct download:
- The raw digital gene expression matrix of the high quality cells (UMI counts).
- The normalized digital gene expression matrix of the high quality cells.
- The binarized and continuous in situ database (BDTNP).
- The bin locations within the embryo used for visualization.
- DistMap and instructions to install and use it can be found on GitHub.
- Genome tracks of the in silico dissected clusters and germ layers.
Loading data ... (DVEX is currently better supported on Linux / Mac OS X)
Drosophila Virtual Expression eXplorer
DVEX is an online resource tool which offers an easy way to explore the transcriptome of the stage 6 Drosophila embryo at the single cell level. It is part of the collaboration between the Rajewsky and Zinzen labs in the Berlin Institute of Medical Systems Biology of the Max Delbrueck Center in Berlin. DVEX accompanies the following publication:
Science 358 (6360), 194-199
The Drosophila Embryo at Single Cell Transcriptome Resolution
Nikos Karaiskosa, Philipp Wahleb, Jonathan Allesa, Anastasiya Boltengagena, Salah Ayouba, Claudia Kiparb, Christine Kocksa, Nikolaus Rajewskya, Robert Zinzenb,
aSystems biology of gene regulatory elements, BIMSB, MDC
bSystems biology of neural tissue differentiation, BIMSB, MDC
Correspondence regarding the publication: Nikolaus Rajewsky and Robert P. Zinzen.
DVEX is created and maintained by Nikos Karaiskos. Contact the author for questions, or troubleshooting.
Technical setting
The coordinate system used for visualization of gene patterns in DVEX comes from the BDTNP project, in which the 3D positions of 6,000 nuclei were registered.
The spatial mapping of the single cells was performed with DistMap, a mapping strategy based on distributed scores developed from Nikos Karaiskos for the purposes of the above publication and of DVEX.
Note that ubiquitous genes are not yet fully supported and their expression pattern can appear misleading, since DVEX is mainly designed to predict patterned genes. Potentially ubiquitous genes are flagged as such.
Up to 20 concurrent user connections are currently supported.
DVEX features
DVEX offers currently the following features:
- t-SNE: a two-dimensional representation of the D. melanogaster high-quality cells, the location of cell populations on the embryo and plotting of gene expression levels on the t-SNE representation for any given gene that was detected. t-SNE and vISH contain complementary information and both should be used when predicting patterns of unstudied genes.
- vISH: the virtual in situ hybridization can be used to predict spatial expression patterns for any given gene that was detected. The threshold controls the number of locations considered. vISH supports currently five different embryo orientations.
- vISHs: prediction of spatial expression patterns for two genes at the same time.
- vISH - D. vir: prediction of spatial expression patterns for the D. vir.
- Gradients: expression gradients for the D. mel. genes. The sliders trim the embryo along the two axes symmetrically, i.e. a value of slider_x=15 corresponds to restricting the embryo at the middle 70% of the anteroposterior axis.
- Archetypes: find sets of spatially related genes. Given a gene and a threshold (as found by inspecting the respective vISH), identify the genes which are expressed in the same spatial domain.
DVEX currently offers quantification and spatial expression of 8924 protein-coding genes and lncRNAs. Note that those should be queried by their respective gene symbols (Ensembl release 86). Alternate names, synonymes, CGs, and FBGNs are not yet supported and should be converted, e.g. at FlyBase.
Release notes
- 5 September 2018: we added the Archetypes section to find spatially related genes.
- 19 February 2018: loading and operating times significantly reduced.
- 22 August 2017: we added flagging of potentially ubiquitous genes and the Download section.
- 17 March 2017: DVEX goes online.