Digital development

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

Anthony Santella, Ismar Kovacevic, Laura A. Herndon, David H. Hall, Zhuo Du, Zhirong Bao

Research output: Contribution to journalArticle

2 Citations (Scopus)

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, cellspecific 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

Original languageEnglish (US)
Pages (from-to)D781-D785
JournalNucleic Acids Research
Volume44
Issue numberD1
DOIs
StatePublished - 2016

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Cell Lineage
Cell Differentiation
Databases
Phenotype
Developmental Biology
Genes
Cell Tracking
Systems Biology
Gene Regulatory Networks
Genomics
Embryonic Structures

ASJC Scopus subject areas

  • Genetics

Cite this

Digital development : A database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model. / Santella, Anthony; Kovacevic, Ismar; Herndon, Laura A.; Hall, David H.; Du, Zhuo; Bao, Zhirong.

In: Nucleic Acids Research, Vol. 44, No. D1, 2016, p. D781-D785.

Research output: Contribution to journalArticle

Santella, Anthony ; Kovacevic, Ismar ; Herndon, Laura A. ; Hall, David H. ; Du, Zhuo ; Bao, Zhirong. / Digital development : A database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model. In: Nucleic Acids Research. 2016 ; Vol. 44, No. D1. pp. D781-D785.
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