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Nucleic Acids Res. 2016 Jan 4;44(D1):D781-5. doi: 10.1093/nar/gkv1119. Epub 2015 Oct 25.

Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model.

Author information

1
Sloan Kettering Institute, New York, NY 10065, USA.
2
Albert Einstein College of Medicine, Bronx, NY 10461, USA.
3
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China zdu@genetics.ac.cn.
4
Sloan Kettering Institute, New York, NY 10065, USA baoz@mskcc.org.

Abstract

Developmental systems biology is poised to exploit large-scale data from two approaches: genomics and live imaging. The combination of the two offers the opportunity to map gene functions and gene networks in vivo at single-cell resolution using cell tracking and quantification of cellular phenotypes. Here we present Digital Development (http://www.digital-development.org), a database of cell lineage differentiation with curated phenotypes, cell-specific gene functions and a multiscale model. The database stores data from recent systematic studies of cell lineage differentiation in the C. elegans embryo containing ∼ 200 conserved genes, 1400 perturbed cell lineages and 600,000 digitized single cells. Users can conveniently browse, search and download four categories of phenotypic and functional information from an intuitive web interface. This information includes lineage differentiation phenotypes, cell-specific gene functions, differentiation landscapes and fate choices, and a multiscale model of lineage differentiation. Digital Development provides a comprehensive, curated, multidimensional database for developmental biology. The scale, resolution and richness of biological information presented here facilitate exploration of gene-specific and systems-level mechanisms of lineage differentiation in Metazoans.

PMID:
26503254
PMCID:
PMC4702815
DOI:
10.1093/nar/gkv1119
[Indexed for MEDLINE]
Free PMC Article

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