Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
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Transcript of Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
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The Mouse Gene Expression Database (GXD)
Martin Ringwald
The Jackson Laboratory
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Mouse developmental gene expression data provide insights into
• organismal function of genes
• molecular mechanism of differentiation
• molecular basis of disease
Genotype Phenotype Expression
Mouse Strains and Mutants
Of mice and men …..
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• integrates different types of expression data
RNA in situ hybridization Northern blot
Immunohistochemistry Western blot
Knock-in reporter studies RT-PCR
• focus on endogenous gene expression
during mouse development
• all developmental stages
• expression data from wild-type and mutant mice
The Gene Expression Database (GXD)
Gene
RNA
Protein
1…n
1…p
Time Space
Genotype
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Standardized description of expression patterns
Hierarchical structure: • Extensibility • Hierarchical searches • Integrated description of expression patterns from assays with differing spatial resolution
Anatomical Ontology for Mouse Development: developed by Edinburgh Mouse Atlas Project maintained and expanded by EMAP and GXD
Anatomical Ontology for the Adult Mouse: developed and maintained by GXD
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Integrated access to complex and heterogeneous data to facilitate the use of the mouse as an experimental model to study human development and disease.
Integration with all the other data in MGI
Genotype Phenotype Expression
Function!
PubMed
OMIM
GenBank/EMBL/DDBJ
Entrez Gene
UniProt
InterPro
EMAGE
GenePaint
GEO
Array Express
IMSR
Other species DB
Many links to other resources:
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MGI Home Page: www.informatics.jax.org
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GXD Home Page
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• Data Acquisition and Current Data Content
• New Search and Display Features
Recent Progress
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• curation of expression data from literature
• electronic submission from laboratories – small and large scale data
• collaboration with projects that generate data at a large scale
Data Acquisition for GXD
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First step of literature curation: Each article is indexed with regard to - Genes - Assay types - Embryonic ages - Bibliographic information
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as of 6/15/13: 149,941 entries 20,996 references 15,033 genes up-to-date complete from 1993 (1990) to the present
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Superior to PubMed: • Manual annotation of whole manuscript • Use of standard gene nomenclature • Indexing of assay types and embryonic ages
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Primary Image Data
Example: RT-PCR
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Primary Image Data
Example: Immunohistochemistry
Sections
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Antibody detail
Gene
Specimens
Mutant "alleles
Results
Link to"images
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• Standard nomenclature • Extensive use of controlled vocabularies • Manual and computational consistency checks • Editorial Interface and QC reports • Detailed and regularly updated editorial guidelines
Data Quality Control
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Data Quality Control
• Text-based annotations complemented by primary image data • Annotations are NOT based on our own interpretation of the images. They strictly rely on the statements of the authors. • Resolution of annotations is determined by details provided in the text of the manuscript. • We notify authors once data for their publications have been entered. Authors can provide comments and additional information.
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Gene Expression Data – Result Annotations
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Large-scale Gene Expression Data Sets
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Incorporation of large-scale data sets
• Develop parsers to extract and evaluate data • Manual and computational quality controls - verify gene identity: probe to gene mapping - verify probe identity: probe already in database? - map results to anatomical ontology and other controlled vocabularies - resolve ambiguities - complete annotations • Bring data in standardized format for data loads • Bulk-load curated data in GXD
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GXD adds value to large-scale data sets
from other databases
• data are integrated with all the other data in GXD and MGI • data are accessible via many new search parameters • data and data connections are maintained and kept up-to-date
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GXD: Current Data Content
249,010 Expression Images 1,394,685 Annotated Expression Results 63,374 Expression Assays 13,751 Genes 1,820 Mouse Mutants with Expression Data
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• Gene Expression Data Query Forms
• Expression Data Summaries
• Expression Assay Details
• Images
Improved Search and Display Capabilities
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MGI
Gene Detail Page
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Function (GO) Phenotype Disease
Anatomy Dev. Stage Age
Wild-type / mutant
Assay type
New Query Form - Standard Search
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New Query Form - Differential Expression Search
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Function (GO) Phenotype Disease
Anatomy Dev. Stage Age
Wild-type / mutant
Assay type
New Query Form - Standard Search
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1824 genes annotated to DNA binding Expression data are available for this gene set (otherwise ‘DNA binding’ would be greyed out).
Auto-fill function
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DNA binding genes
detected in
diencephalon at TS 17-20
by Immunohistochemistry
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New Summary – Assay Results
• 4 sortable data summaries: genes, assays, assay results, images • links to detailed annotations and images • summary data can be downloaded and exported to other applications
Sort
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New Summary – Assays
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New Summary – Genes
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New Summary – Assay Results
• 4 sortable data summaries: genes, assays, assay results, images • links to detailed annotations and images • summary data can be downloaded and exported to other applications
Sort
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Previous Assay Details
reference to 1H, 1J; link to Figure 1
all specimen information displayed upfront
reference to 1E, 1F; link to Figure 1
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Links to 3-D mapped images in EMAGE 46
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New Assay Details
focus on most important specimen information
images displayed together with result annotations
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New Summary – Images
Search directly for images using many different query criteria
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New Summary – Images
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New Assay Details
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• Gene Expression Data Query Forms
- improved layout
- new query capabilities
• Strongly enhanced query performance
• Expression Data Summaries
- more flexible and interactive
- option to download and export data
- image summaries
• Expression Assay Details
- integration of images and annotations
- improved layout - focus on essential data
Improved Search and Display Capabilities
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• MGI Batch Query
• GXD BioMart
New ways to access GXD Data
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• Enter list of gene symbols or IDs and look up associated expression data
• Download data and export data to other applications
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GXD BioMart
Find expression data • for a gene • for a list of genes • for an anatomical structure • for a mutant • for a reference Integrated searches across different BioMarts
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GXD BioMart: Query Results (default view)
Export Data
Link to Images Link to Assay Details
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Constance Smith Jacqueline Finger Terry Hayamizu Ingeborg McCright Jingxia Xu David Shaw Joanne Berghout MGI Software Group Jim Kadin Joel Richardson Janan Eppig
Acknowledgements
GXD is supported by NICHD