title: SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos.
abstract: We present SuperFly (http://superfly.crg.eu), 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 mechanistic understanding of developmental evolution.
authors.affiliation: EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
authors.forename: Damjan
authors.initials: D
authors.lastname: Cicin-Sain
authors.affiliation: Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
authors.forename: Antonio Hermoso
authors.initials: AH
authors.lastname: Pulido
authors.affiliation: EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
authors.forename: Anton
authors.initials: A
authors.lastname: Crombach
authors.affiliation: EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
authors.forename: Karl R
authors.initials: KR
authors.lastname: Wotton
authors.affiliation: EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Jiménez-Guri
authors.affiliation: Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Taly
authors.affiliation: Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
authors.forename: Guglielmo
authors.initials: G
authors.lastname: Roma
authors.affiliation: EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain yogi.jaeger@crg.eu.
authors.forename: Johannes
authors.initials: J
authors.lastname: Jaeger
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D004175:Diptera / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics; D004625:Embryo, Nonmammalian / Q000378:metabolism; D015870:Gene Expression; D020407:Internet