The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

Hayamizu, Terry F.; Mangan, Mary; Corradi, John P.; Kadin, James A.; Ringwald, Martin

doi:10.1186/gb-2005-6-3-r29

Cited by 155 publications

(78 citation statements)

References 13 publications

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“…34,36 In MoDIS, anatomical structures (ie, organs) are defined using the Mouse Anatomy Ontology (MA), 11 and histopathological lesions are defined according to the Mouse Pathology Ontology (MPATH). 28 Representative photomicrographs of lesions are available on Pathbase (http://www.pathbase.net/) and in the Mouse Tumor Biology Database (MTB) (http://www.informatics.jax.org/).…”

Section: Methodsmentioning

confidence: 99%

Phenotypic Characterization of the KK/HlJ Inbred Mouse Strain

et al. 2013

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Detailed histopathological diagnoses of inbred mouse strains are important for interpreting research results and defining novel models of human diseases. The aim of this study was to histologically detect lesions affecting the KK/HlJ inbred strain. Mice were examined at 6, 12, and 20 months of age and near natural death (ie, moribund mice). Histopathological lesions were quantified by percentage of affected mice per age group and sex. Predominant lesions were mineralization, hyperplasia, and fibro-osseous lesions. Mineralization was most frequently found in the connective tissue dermal sheath of vibrissae, the heart, and the lung. Mineralization was also found in many other organs but to a lesser degree. Hyperplasia was found most commonly in the pancreatic islets, and fibro-osseous lesions were observed in several bones. The percentage of lesions increased with age until 20 months. This study shows that KK/HlJ mice demonstrate systemic aberrant mineralization, with greatest frequency in aged mice. The detailed information about histopathological lesions in the inbred strain KK/HlJ can help investigators to choose the right model and correctly interpret the experimental results.

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Section: Methodsmentioning

confidence: 99%

Phenotypic Characterization of the KK/HlJ Inbred Mouse Strain

et al. 2013

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“…Expression patterns are described using an extensive dictionary of standardized anatomical terms that lists the anatomical structures for each developmental stage in a hierarchical fashion, thus enabling the recording of expression results from assays with different spatial resolution in a consistent manner. The embryonic part of the anatomical dictionary was developed by our collaborators from the Edinburgh Mouse Atlas and Gene Expression Database (EMAGE) project (31); the adult part was developed by the GXD project (32). As well as enabling complex querying capabilities, these detailed annotations make it easier to interpret and compare expression data.…”

Section: Data Contentmentioning

confidence: 99%

The mouse Gene Expression Database (GXD): 2007 update

Smith

Finger

Hayamizu

et al. 2007

Nucleic Acids Research

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The Gene Expression Database (GXD) provides the scientific community with an extensive and easily searchable database of gene expression information about the mouse. Its primary emphasis is on developmental studies. By integrating different types of expression data, GXD aims to provide comprehensive information about expression patterns of transcripts and proteins in wild-type and mutant mice. Integration with the other Mouse Genome Informatics (MGI) databases places the gene expression information in the context of genetic, sequence, functional and phenotypic information, enabling valuable insights into the molecular biology that underlies developmental and disease processes. In recent years the utility of GXD has been greatly enhanced by a large increase in data content, obtained from the literature and provided by researchers doing large-scale in situ and cDNA screens. In addition, we have continued to refine our query and display features to make it easier for users to interrogate the data. GXD is available through the MGI web site at or directly at .

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“…Slides were reviewed and diagnoses were entered and coded by individual mouse using the Mouse Disease Information System (MoDIS) (Sundberg et al, 2009; Sundberg et al, 2008). Anatomical structures were defined using the Mouse Anatomy Ontology (MA) (Hayamizu et al, 2005) and disease diagnoses were entered using the Mouse Pathology ontology (MPATH) (Schofield et al, 2010a; Schofield et al, 2010b). Representative images of lesions in addition to those presented here are available on Pathbase (http://www.pathbase.net/) (Schofield et al, 2004a; Schofield et al, 2004b; Schofield et al 2010b) and in the Mouse Tumor Biology Database (http://tumor.informatics.jax.org/) (Begley et al, 2014; Krupke et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

Genetic determinants of fibro-osseous lesions in aged inbred mice

Berndt

Ackert‐Bicknell

Silva

et al. 2016

Experimental and Molecular Pathology

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Fibro-osseous lesions in mice are progressive aging changes in which the bone marrow is replaced to various degrees by fibrovascular stroma and bony trabeculae in a wide variety of bones. The frequency and severity varied greatly among 28 different inbred mouse stains, predominantly affecting females, ranging from 0% for 10 strains to 100% for KK/HlJ and NZW/LacJ female mice. Few lesions were observed in male mice and for 23 of the strains, no lesions were observed in males for any of the cohorts. There were no significant correlations between strain-specific severities of fibro-osseous lesions and ovarian (r=0.11; P=0.57) or endometrial (r=0.03; P=0.89) cyst formation frequency or abnormalities in parathyroid glands. Frequency of fibro-osseous lesions was most strongly associated (P < 10−6) with genome variations on chromosome (Chr) 8 at 90.6 and 90.8 Mb (rs33108071, rs33500669; P = 5.0 · 10−10, 1.3 · 10−6), Chr 15 at 23.6 and 23.8 Mb (rs32087871, rs45770368; P = 7.3 · 10−7, 2.7 · 10−6), and Chr 19 at 33.2, 33.4, and 33.6 Mb (rs311004232, rs30524929, rs30448815; P=2.8 · 10−6, 2.8 · 10−6, 2.8 · 10−6) in genome-wide association studies (GWAS). The relatively large number of candidate genes identified in the GWAS analyses suggests that this may be an extremely complex polygenic disease. These results indicate that fibro-osseous lesions are surprisingly common in many inbred strains of laboratory mice as they age. While this presents little problem in most studies that utilize young animals, it may complicate aging studies, particularly those focused on bone.

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The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

Cited by 155 publications

References 13 publications

Phenotypic Characterization of the KK/HlJ Inbred Mouse Strain

Phenotypic Characterization of the KK/HlJ Inbred Mouse Strain

The mouse Gene Expression Database (GXD): 2007 update

Genetic determinants of fibro-osseous lesions in aged inbred mice

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