mouse anatomy ontologies and gxd

Terry F. HayamizuMouse Genome Informatics, The Jackson Laboratory

MOUSE ANATOMY ONTOLOGIES AND GXD

Gene Expression Database (GXD)

Currently, GXD includes:• a comprehensive literature index for mouse

gene expression, with a primary emphasis on endogenous expression during embryonic development, covering >14,000 genes studied in >18,500 primary references

• detailed experimental data for >12,700 mouse genes in >50,000 expression assays from ~5000 references, including data for >1,500 mouse mutants, as well as >200,000 images associated with expression data

• over 1 million gene expression results annotated to specific mouse anatomy terms

Stage i

Stage j

S

T V

X Y

U

stage-dependent

DAGsstage-

independentDAG

EMAPA

s

x

s

x y

t vu

vu

Ww

EMAP

anatomy ontology for

mouse development

developed by EMAP

anatomy ontology for the postnatal mouse

developed by GXD

Represent develops-from relationships

EMAP /EMAPA

MA

TS X

TS Y

“develops-from” relationships

TS 28

GENOTYPE

PHENOTYPE

GENETICS

DISEASE MODELS

GENE EXPRESSION

Anatomy

Gene Expression Phenotype

Biological Process

Disease

Pathological Process

Adult Mouse Anatomy

Gene Expression Database

Mammalian Phenotype ontology

Pathbase

Gene Ontology NCI Thesaurus

Pathological Process

Biological Process

Anatomy

Anatomy

Anatomy

Gene Expression

Biological Process

Phenotype

Disease

Gene ExpressionPhenotype

Pathological Process Disease

Gene Expression

Biological Process

Phenotype

Pathological Process

Disease

Anatomical ontologies from other species

Other Mouse Genome Informatics (MGI) resources

Mammalian Phenotype Ontology (MP)

Gene Ontology (GO)Cell Ontology (CO)

Edinburgh Mouse Atlas Project (EMAP)

Duncan DavidsonRichard BaldockJonathan Bard

Matthew Kaufman

Gene Expression Database (GXD)

Martin RingwaldJanan EppigJim Kadin

Joel Richardson

Jacqueline FingerIngeborg McCrightConstance Smith

Jingxia Xu

Acknowledgements

GXD is funded by NIH/NICHD grant HD033745