Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model.
Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model.
复制标题
数字开发：线虫细胞谱系分化数据库，包括谱系表型、细胞特异性基因功能和多尺度模型。
DOI：
10.1093/nar/gkv1119
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Bao Z
中科院分区：
文献类型：
--
作者：
Santella A;Kovacevic I;Herndon LA;Hall DH;Du Z;Bao Z
发育系统生物学准备利用两种方法的大规模数据：基因组学和实时成像。两者的结合提供了利用细胞跟踪和细胞表型定量在单细胞分辨率下绘制基因功能和基因网络的机会。在这里，我们提出数字发展（http://www.digital-development.org），细胞谱系分化与策展表型，细胞特异性基因功能和多尺度模型的数据库。该数据库存储了最近对秀丽隐杆线虫胚胎细胞系分化的系统研究数据，其中包含约200个保守基因，1400个受干扰的细胞系和60万个数字化单细胞。用户可以通过直观的web界面方便地浏览、搜索和下载四类表型和功能信息。这些信息包括谱系分化表型，细胞特异性基因功能，分化景观和命运选择，以及谱系分化的多尺度模型。数字发展为发育生物学提供了一个全面的、精心策划的多维数据库。这里提供的生物信息的规模、分辨率和丰富性有助于探索后生动物谱系分化的基因特异性和系统水平机制。
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.