Terry F. Hayamizu Mouse Genome Informatics, The Jackson Laboratory MOUSE ANATOMY ONTOLOGIES AND GXD
Feb 23, 2016
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