More than a decade of developmental gene expression atlases: where are we now? Export

@article{citeulike:5936100, abstract = {To unravel regulatory networks of genes functioning during embryonic development, information on in situ gene expression is required. Enormous amounts of such data are available in literature, where each paper reports on a limited number of genes and developmental stages. The best way to make these data accessible is via spatio-temporal gene expression atlases. Eleven atlases, describing developing vertebrates and covering at least 100 genes, were reviewed. This review focuses on: (i) the used anatomical framework, (ii) the handling of input data and (iii) the retrieval of information. Our aim is to provide insights into both the possibilities of the atlases, as well as to describe what more than a decade of developmental gene expression atlases can teach us about the requirements of the design of the ideal atlas'. This review shows that most ingredients needed to develop the ideal atlas are already applied to some extent in at least one of the discussed atlases. A review of these atlases shows that the ideal atlas should be based on a spatial framework, i.e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution, both for relations as well as for anatomical terms. 10.1093/nar/gkp819}, author = {de Boer, Bouke A. and Ruijter, Jan M. and Voorbraak, Frans P. J. M. and Moorman, Antoon F. M.}, citeulike-article-id = {5936100}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkp819}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/gkp819v1/.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/gkp819v1/.full.pdf}, citeulike-linkout-3 = {http://nar.oxfordjournals.org/cgi/content/abstract/37/22/7349}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19822576}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19822576}, day = {1}, doi = {10.1093/nar/gkp819}, issn = {1362-4962}, journal = {Nucl. Acids Res.}, keywords = {database, geneexpression}, month = {December}, number = {22}, pages = {7349--7359}, posted-at = {2009-10-16 10:31:48}, priority = {3}, title = {More than a decade of developmental gene expression atlases: where are we now?}, url = {http://dx.doi.org/10.1093/nar/gkp819}, volume = {37}, year = {2009} }

TY - JOUR ID - citeulike:5936100 L3 - citeulike-article-id:5936100 N2 - To unravel regulatory networks of genes functioning during embryonic development, information on in situ gene expression is required. Enormous amounts of such data are available in literature, where each paper reports on a limited number of genes and developmental stages. The best way to make these data accessible is via spatio-temporal gene expression atlases. Eleven atlases, describing developing vertebrates and covering at least 100 genes, were reviewed. This review focuses on: (i) the used anatomical framework, (ii) the handling of input data and (iii) the retrieval of information. Our aim is to provide insights into both the possibilities of the atlases, as well as to describe what more than a decade of developmental gene expression atlases can teach us about the requirements of the design of the ideal atlas'. This review shows that most ingredients needed to develop the ideal atlas are already applied to some extent in at least one of the discussed atlases. A review of these atlases shows that the ideal atlas should be based on a spatial framework, i.e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution, both for relations as well as for anatomical terms. 10.1093/nar/gkp819 IS - 22 JF - Nucl. Acids Res. SN - 1362-4962 EP - 7359 TI - More than a decade of developmental gene expression atlases: where are we now? VL - 37 SP - 7349 KW - database KW - geneexpression AU - de Boer, Bouke AU - Ruijter, Jan AU - Voorbraak, Frans AU - Moorman, Antoon PY - 2009/12/01/ UR - http://dx.doi.org/10.1093/nar/gkp819 ER -