SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos

Nucleic Acids Research
Damjan Cicin-SainJohannes Jaeger


We present SuperFly (, a relational database for quantified spatio-temporal expression data of segmentation genes during early development in different species of dipteran insects (flies, midges and mosquitoes). SuperFly has a special focus on emerging non-drosophilid model systems. The database currently includes data of high spatio-temporal resolution for three species: the vinegar fly Drosophila melanogaster, the scuttle fly Megaselia abdita and the moth midge Clogmia albipunctata. At this point, SuperFly covers up to 9 genes and 16 time points per species, with a total of 1823 individual embryos. It provides an intuitive web interface, enabling the user to query and access original embryo images, quantified expression profiles, extracted positions of expression boundaries and integrated datasets, plus metadata and intermediate processing steps. SuperFly is a valuable new resource for the quantitative comparative study of gene expression patterns across dipteran species. Moreover, it provides an interesting test set for systems biologists interested in fitting mathematical gene network models to data. Both of these aspects are essential ingredients for progress toward a more quantitative and mechanisti...Continue Reading


Jan 24, 1992·Cell·D St Johnston, C Nüsslein-Volhard
Sep 1, 1993·Cell and Tissue Research·P GreenV Hartenstein
Jan 27, 1998·Seminars in Cell & Developmental Biology·W Janning
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·Michael StauberUrs Schmidt-Ott
Sep 20, 2000·Proceedings of the National Academy of Sciences of the United States of America·Michael StauberUrs Schmidt-Ott
Apr 3, 2004·Bioinformatics·Ekaterina PoustelnikovaJohn Reinitz
Jul 7, 2007·Genome Biology·Rachel LyneGos Micklem
Dec 11, 2007·Developmental Biology·Svetlana SurkovaJohn Reinitz
Jan 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ab Matteen RafiqiUrs Schmidt-Ott
Jan 25, 2008·Development Genes and Evolution·Michael StauberUrs Schmidt-Ott
Jul 22, 2008·Evolution & Development·Steffen LemkeUrs Schmidt-Ott
Oct 28, 2008·Nucleic Acids Research·Andrei PisarevJohn Reinitz
Feb 14, 2009·The FEBS Journal·Maksat AshyraliyevJoke G Blom
May 1, 2010·Development·Steffen LemkeUrs Schmidt-Ott
May 4, 2010·Developmental Biology·Mónica A García-SolacheMichael Akam
Oct 12, 2010·Cellular and Molecular Life Sciences : CMLS·Johannes Jaeger
Oct 22, 2010·BMC Bioinformatics·Vijender ChaitankarChaoyang Zhang
Jul 19, 2012·PLoS Computational Biology·Anton CrombachJohannes Jaeger
Aug 10, 2012·Development·Ab Matteen RafiqiUrs Schmidt-Ott
Dec 4, 2012·Nucleic Acids Research·Scott W RobinsonDavid P Leader
Jan 24, 2013·Molecular Systems Biology·Julien O DubuisThomas Gregor
Feb 26, 2013·BMC Genomics·Eva Jiménez-GuriJohannes Jaeger
Apr 19, 2013·Development Genes and Evolution·Karl R WottonEva Jiménez-Guri
Nov 10, 2013·PLoS Computational Biology·Kolja BeckerJohannes Jaeger
Nov 16, 2013·Nucleic Acids Research·Susan E St PierreFlyBase Consortium
Dec 7, 2013·Journal of the Royal Society, Interface·Alejandro F Villaverde, Julio R Banga
Jan 11, 2014·PloS One·Karl R WottonJohannes Jaeger
Jan 11, 2014·PloS One·Eva Jiménez-GuriJohannes Jaeger


Jan 23, 2016·Molecular Biology and Evolution·Anton CrombachJohannes Jaeger
Jul 12, 2016·Current Opinion in Genetics & Development·Urs Schmidt-Ott, Jeremy A Lynch
Oct 3, 2019·Proceedings. Biological Sciences·Ariel D Chipman, Gregory D Edgecombe

Methods Mentioned


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Drosophila melanogaster
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