ReviewNucleic acids research2009
More than a decade of developmental gene expression atlases: where are we now?
Review in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Prune homolog 2 with BCH domain (PRUNE2) gene expression is associated with feed efficiency-related traits in Nelore steers.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Article
- EmExplorer: a database for exploring time activation of gene expression in mammalian embryos.Open biology · 2019Article
- Leveraging Online Resources to Prioritize Candidate Genes for Functional Analyses: Using the Fetal Testis as a Test Case.Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation · 2017Review
- Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design.BMC developmental biology · 2016Article
- Constrained distance transforms for spatial atlas registration.BMC bioinformatics · 2015Article
- Comparing mRNA levels using in situ hybridization of a target gene and co-stain.Methods (San Diego, Calif.) · 2014Article
- A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis.PLoS computational biology · 2014Article
- EMAGE mouse embryo spatial gene expression database: 2014 update.Nucleic acids research · 2014Article
- A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development.Frontiers in neuroscience · 2014Article
- METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters.Nucleic acids research · 2013Article
- Web-based digital gene expression atlases for the mouse.Mammalian genome : official journal of the International Mammalian Genome Society · 2012Review
- iSyTE: integrated Systems Tool for Eye gene discovery.Investigative ophthalmology & visual science · 2012Article
- Site-specific integration and tailoring of cassette design for sustainable gene transfer.Nature methods · 2011Article
- SCLD: a Stem Cell Lineage Database for the annotation of cell types and developmental lineages.Nucleic acids research · 2011Article
- The interactive presentation of 3D information obtained from reconstructed datasets and 3D placement of single histological sections with the 3D portable document format.Development (Cambridge, England) · 2011Article
- The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain.Journal of anatomy · 2010Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.