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.
The following data is available for direct download:
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
DVEX is created and maintained by Nikos Karaiskos. Contact the author for questions, or troubleshooting.
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 offers currently the following features:
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.