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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. DVEX is part of the following work:

The Drosophila Embryo at Single Cell Transcriptome Resolution

Nikos Karaiskos, Philipp Wahle, Jonathan Alles, Anastasiya Boltengagen, Salah Ayoub, Claudia Kipar, Christine Kocks, Nikolaus Rajewsky and Robert P. Zinzen

Correspondence: Nikolaus Rajewsky and Robert P. Zinzen.
DVEX is created and maintained by Nikos Karaiskos.

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.
  • 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 views.
  • 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 looking only at the middle 70% of the embryo, regarding the AP axis.

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.

Note that ubiquitous genes are not yet fully supported and their vISH can appear misleading. Although lowering the threshold to 0 resolves the problems in some of these cases, DVEX is mainly designed and targeted to patterned genes.