The Mouse Gene Expression Database
(GXD)
Martin Ringwald
The Jackson Laboratory
Mouse developmental gene expression data provide insights into
• organismal function of genes
• molecular mechanism of dif...
• integrates different types of expression data
RNA in situ hybridization Northern blot
Immunohistochemistry Western blot
...
Standardized description of expression patterns
Hierarchical structure:
• Extensibility
• Hierarchical searches
• Integrat...
Integrated access to complex and heterogeneous data
to facilitate the use of the mouse as an experimental
model to study h...
MGI Home Page: www.informatics.jax.org
GXD Home Page
• Data Acquisition and Current Data Content
• New Search and Display Features
Recent Progress
• curation of expression data from literature
• electronic submission from laboratories – small and large scale data
• col...
First step of literature curation:
Each article is indexed with regard to
-  Genes
-  Assay types
-  Embryonic ages
-  Bib...
as of 6/15/13:
149,941 entries
20,996 references
15,033 genes
up-to-date
complete from
1993 (1990) to
the present
Superior to PubMed:
• Manual annotation of whole manuscript
• Use of standard gene nomenclature
• Indexing of assay types ...
Primary
Image Data
Example: RT-PCR
Primary
Image Data
Example:
Immunohistochemistry
Sections
Antibody detail
Gene
Specimens
Mutant "
alleles
Results
Link to"
images
• Standard nomenclature
• Extensive use of controlled vocabularies
• Manual and computational consistency checks
• Editori...
Data Quality Control
• Text-based annotations complemented by primary image data
• Annotations are NOT based on our own in...
Gene Expression Data – Result Annotations
Large-scale Gene Expression Data Sets
Incorporation of large-scale data sets
• Develop parsers to extract and evaluate data
• Manual and computational quality c...
GXD adds value to large-scale data sets
from other databases
• data are integrated with all the other data in GXD and MGI
...
GXD: Current Data Content
249,010 Expression Images
1,394,685 Annotated Expression Results
63,374 Expression Assays
13,751...
• Gene Expression Data Query Forms
• Expression Data Summaries
• Expression Assay Details
• Images
Improved Search and Dis...
MGI
Gene Detail
Page
Function (GO)
Phenotype
Disease
Anatomy
Dev. Stage
Age
Wild-type / mutant
Assay type
New Query Form - Standard Search
New Query Form - Differential Expression Search
Function (GO)
Phenotype
Disease
Anatomy
Dev. Stage
Age
Wild-type / mutant
Assay type
New Query Form - Standard Search
1824 genes annotated to
DNA binding
Expression data are
available for this gene set
(otherwise ‘DNA binding’
would be grey...
DNA binding genes
detected in
diencephalon
at TS 17-20
by Immunohistochemistry
New Summary – Assay Results
• 4 sortable data summaries: genes, assays, assay results, images
• links to detailed annotati...
New Summary – Assays
New Summary – Genes
New Summary – Assay Results
• 4 sortable data summaries: genes, assays, assay results, images
• links to detailed annotati...
45
Previous
Assay Details
reference to 1H, 1J; link to Figure 1
all specimen information
displayed upfront
reference to 1E...
Links to 3-D mapped
images in EMAGE 46
45
New
Assay Details
focus on most important
specimen information
images displayed together
with result annotations
New Summary – Images
Search directly
for images using
many different
query criteria
New Summary – Images
45
New
Assay Details
• Gene Expression Data Query Forms
- improved layout
- new query capabilities
• Strongly enhanced query performance
• Expr...
• MGI Batch Query
• GXD BioMart
New ways to access GXD Data
• Enter list of gene symbols or IDs and look up associated expression data
• Download data and export data to other applic...
GXD BioMart
Find expression data
• for a gene
• for a list of genes
• for an anatomical
structure
• for a mutant
• for a r...
GXD BioMart: Query Results (default view)
Export Data
Link to ImagesLink to Assay Details
Constance Smith
Jacqueline Finger
Terry Hayamizu
Ingeborg McCright
Jingxia Xu
David Shaw
Joanne Berghout
MGI Software Grou...
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
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Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013

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Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013

  1. 1. The Mouse Gene Expression Database (GXD) Martin Ringwald The Jackson Laboratory
  2. 2. Mouse developmental gene expression data provide insights into • organismal function of genes • molecular mechanism of differentiation • molecular basis of disease Genotype PhenotypeExpression Mouse Strains and Mutants Of mice and men …..
  3. 3. • 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
  4. 4. 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
  5. 5. 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 PhenotypeExpression Function! PubMed OMIM GenBank/EMBL/DDBJ Entrez Gene UniProt InterPro EMAGE GenePaint GEO Array Express IMSR Other species DB Many links to other resources:
  6. 6. MGI Home Page: www.informatics.jax.org
  7. 7. GXD Home Page
  8. 8. • Data Acquisition and Current Data Content • New Search and Display Features Recent Progress
  9. 9. • 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
  10. 10. First step of literature curation: Each article is indexed with regard to -  Genes -  Assay types -  Embryonic ages -  Bibliographic information
  11. 11. as of 6/15/13: 149,941 entries 20,996 references 15,033 genes up-to-date complete from 1993 (1990) to the present
  12. 12. Superior to PubMed: • Manual annotation of whole manuscript • Use of standard gene nomenclature • Indexing of assay types and embryonic ages
  13. 13. Primary Image Data Example: RT-PCR
  14. 14. Primary Image Data Example: Immunohistochemistry Sections
  15. 15. Antibody detail Gene Specimens Mutant " alleles Results Link to" images
  16. 16. • 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
  17. 17. 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.
  18. 18. Gene Expression Data – Result Annotations
  19. 19. Large-scale Gene Expression Data Sets
  20. 20. 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
  21. 21. 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
  22. 22. 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
  23. 23. • Gene Expression Data Query Forms • Expression Data Summaries • Expression Assay Details • Images Improved Search and Display Capabilities
  24. 24. MGI Gene Detail Page
  25. 25. Function (GO) Phenotype Disease Anatomy Dev. Stage Age Wild-type / mutant Assay type New Query Form - Standard Search
  26. 26. New Query Form - Differential Expression Search
  27. 27. Function (GO) Phenotype Disease Anatomy Dev. Stage Age Wild-type / mutant Assay type New Query Form - Standard Search
  28. 28. 1824 genes annotated to DNA binding Expression data are available for this gene set (otherwise ‘DNA binding’ would be greyed out). Auto-fill function
  29. 29. DNA binding genes detected in diencephalon at TS 17-20 by Immunohistochemistry
  30. 30. 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
  31. 31. New Summary – Assays
  32. 32. New Summary – Genes
  33. 33. 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
  34. 34. 45 Previous Assay Details reference to 1H, 1J; link to Figure 1 all specimen information displayed upfront reference to 1E, 1F; link to Figure 1
  35. 35. Links to 3-D mapped images in EMAGE 46
  36. 36. 45 New Assay Details focus on most important specimen information images displayed together with result annotations
  37. 37. New Summary – Images Search directly for images using many different query criteria
  38. 38. New Summary – Images
  39. 39. 45 New Assay Details
  40. 40. • 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
  41. 41. • MGI Batch Query • GXD BioMart New ways to access GXD Data
  42. 42. • Enter list of gene symbols or IDs and look up associated expression data • Download data and export data to other applications
  43. 43. 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
  44. 44. GXD BioMart: Query Results (default view) Export Data Link to ImagesLink to Assay Details
  45. 45. 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

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