PUBLICATION

GSD: a genetic screen database

Authors
Henrich, T., Ramialison, M., Segerdell, E., Westerfield, M., Furutani-Seiki, M., Wittbrodt, J., Kondoh, H.
ID
ZDB-PUB-040625-8
Date
2004
Source
Mechanisms of Development   121(7-8): 959-963 (Journal)
Registered Authors
Furutani-Seiki, Makoto, Henrich, Thorsten, Kondoh, Hisato, Segerdell, Erik, Westerfield, Monte, Wittbrodt, Jochen
Keywords
Mutant screen, Medaka, Zebrafish, Phenotype, Ontology
MeSH Terms
  • Animals
  • Databases, Genetic*
  • Gene Expression
  • Internet
  • Mutation
  • Oryzias/embryology
  • Oryzias/genetics*
  • Phenotype
  • Software*
  • Zebrafish/genetics
PubMed
15210199 Full text @ Mech. Dev.
Abstract
The systematic assignment of gene function to a sequenced genome is one of the outstanding challenges in the post-genomic era. Large-scale systematic mutagenesis screens are important tools for reaching this goal. Here we describe GSD, a software package that allows storage and integration of data from genetic screens. GSD was initially developed for a large-scale F3 mutagenesis screen for developmental mutants of medaka (Oryzias latipes). The version presented here supports a wide range of different screens (mutagenesis, RNAi, morpholinos, transgenesis and others) using different organisms. Data are stored in a relational database and can be made accessible through web interfaces. Researchers can enter data describing their screened embryos: They can track statistics, submit images and describe the resulting phenotypes using a phenotype classification ontology. We developed a fish phenotype classification ontology of medaka and zebrafish for this software package and made it available to the public. In addition, a list of genetic lines resulting from each screen can be generated. These lines (mutant alleles, transgenic lines) can be described and categorized in the same ways as the screened individuals. Raw data from the screen can be integrated to describe these lines. A query module that searches this list can be used to publish the screen results on the Internet. A test version is available at and the software can be downloaded from this site.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes