The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.

Area of Science:

• Developmental biology
• Systems biology
• Genomics

Background:

• Current model organism databases lack integration of heterogeneous data across scales.
• Understanding embryonic development requires linking genomic information to subcellular phenotypes.

Purpose of the Study:

• To present a novel, generic digital system (NISEED) and its implementation (ANISEED) for ascidian developmental systems biology.
• To integrate diverse anatomical and molecular data for a global view of the developmental program.

Main Methods:

• Development of ANISEED, a system integrating anatomical ontologies, 3D quantitative geometry, gene expression patterns, and cis-regulatory regions.
• Utilizing a Developmental Browser, Genome Browser, and 3D Virtual Embryo module for data exploration.

Main Results:

• ANISEED hosts an unprecedented combination of data for ascidian development, including detailed anatomical ontologies and 3D cell geometry.
• Integration of 30,000 gene expression patterns and 528 cis-regulatory regions.
• Demonstrated system-level understanding through automatic inference of gene regulatory interactions and identification of inducing signals.

Conclusions:

• ANISEED facilitates a systems-level understanding of developmental programs by integrating heterogeneous data.
• The system aids in discovering novel aspects of developmental processes, such as asymmetric cell divisions.