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Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level.

Mannil D, Vogt I, Prinz J, Campillos M - Nucleic Acids Res. (2014)

Bottom Line: Some perturbations impair relatively few organ systems while others lead to highly heterogeneous or systemic effects.For perturbations of interest, the database displays the distribution of phenotypic effects across organ systems along with the heterogeneity value and the distance between organ system distributions.The Organ System Heterogeneity DB is thus a platform for the visualization and comparison of organ system level phenotypic effects of drugs, diseases and genes.

View Article: PubMed Central - PubMed

Affiliation: German Center for Diabetes Research, Neuherberg 85764, Germany Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany.

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Representation and depiction of phenotype information at SOC and HLT level. (A) We used the hierarchical information of the MedDRA ontology to map all phenotypic features of a drug, disease or gene to the HLT and SOC level. As an example, we show the mapping of symptoms of the disease Aase Smith syndrome to HLT and SOC levels. After the mapping, the relative frequencies of phenotypes under each SOC and the number of phenotypes under each HLT is shown. (B) Screenshot of the ‘View High Level Term phenotypes’ result page of the Aase Smith syndrome. The phenotypes of the disease at the HLT level, the number of phenotypic traits under the HLT level phenotypes and the corresponding SOCs (indicated by colored squares) are reported. The corresponding parts of (A) and (B) are indicated as ‘a’ (HLT), ‘b’ (Number of Phenotypic features under HLT) and ‘c’ (SOC).
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Figure 2: Representation and depiction of phenotype information at SOC and HLT level. (A) We used the hierarchical information of the MedDRA ontology to map all phenotypic features of a drug, disease or gene to the HLT and SOC level. As an example, we show the mapping of symptoms of the disease Aase Smith syndrome to HLT and SOC levels. After the mapping, the relative frequencies of phenotypes under each SOC and the number of phenotypes under each HLT is shown. (B) Screenshot of the ‘View High Level Term phenotypes’ result page of the Aase Smith syndrome. The phenotypes of the disease at the HLT level, the number of phenotypic traits under the HLT level phenotypes and the corresponding SOCs (indicated by colored squares) are reported. The corresponding parts of (A) and (B) are indicated as ‘a’ (HLT), ‘b’ (Number of Phenotypic features under HLT) and ‘c’ (SOC).

Mentions: We made use of the hierarchical structure of MedDRA (http://www.meddra.org/) to annotate the phenotypic data (disease symptoms, drug side effects and phenotypes of genetic perturbations in mice) at two different levels of granularity, the System Organ Class (SOC) and the HLT level (Figure 2). MedDRA, the Medical Dictionary for Regulatory Activities terminology, is the international medical terminology developed under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). MedDRA trademark is owned by IFPMA on behalf of ICH. The SOC level of MedDRA is the most general and groups all terms according to manifestation site or etiology (e.g. infections) into 26 categories. The HLT level is the most specific aggregation level that groups phenotypic features based upon anatomy, pathology, physiology, etiology or function. As depicted in Figure 2A, the mappings of the phenotypic features to the SOC level are used to derive the organ system distribution plots as well as the organ system heterogeneity value. If desired, the user can inspect the more specific phenotype information at the HLT level in relation to the organ system distribution. These distribution plots are shown in the website along with the number of the annotated phenotypic features (Figure 2B).


Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level.

Mannil D, Vogt I, Prinz J, Campillos M - Nucleic Acids Res. (2014)

Representation and depiction of phenotype information at SOC and HLT level. (A) We used the hierarchical information of the MedDRA ontology to map all phenotypic features of a drug, disease or gene to the HLT and SOC level. As an example, we show the mapping of symptoms of the disease Aase Smith syndrome to HLT and SOC levels. After the mapping, the relative frequencies of phenotypes under each SOC and the number of phenotypes under each HLT is shown. (B) Screenshot of the ‘View High Level Term phenotypes’ result page of the Aase Smith syndrome. The phenotypes of the disease at the HLT level, the number of phenotypic traits under the HLT level phenotypes and the corresponding SOCs (indicated by colored squares) are reported. The corresponding parts of (A) and (B) are indicated as ‘a’ (HLT), ‘b’ (Number of Phenotypic features under HLT) and ‘c’ (SOC).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384019&req=5

Figure 2: Representation and depiction of phenotype information at SOC and HLT level. (A) We used the hierarchical information of the MedDRA ontology to map all phenotypic features of a drug, disease or gene to the HLT and SOC level. As an example, we show the mapping of symptoms of the disease Aase Smith syndrome to HLT and SOC levels. After the mapping, the relative frequencies of phenotypes under each SOC and the number of phenotypes under each HLT is shown. (B) Screenshot of the ‘View High Level Term phenotypes’ result page of the Aase Smith syndrome. The phenotypes of the disease at the HLT level, the number of phenotypic traits under the HLT level phenotypes and the corresponding SOCs (indicated by colored squares) are reported. The corresponding parts of (A) and (B) are indicated as ‘a’ (HLT), ‘b’ (Number of Phenotypic features under HLT) and ‘c’ (SOC).
Mentions: We made use of the hierarchical structure of MedDRA (http://www.meddra.org/) to annotate the phenotypic data (disease symptoms, drug side effects and phenotypes of genetic perturbations in mice) at two different levels of granularity, the System Organ Class (SOC) and the HLT level (Figure 2). MedDRA, the Medical Dictionary for Regulatory Activities terminology, is the international medical terminology developed under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). MedDRA trademark is owned by IFPMA on behalf of ICH. The SOC level of MedDRA is the most general and groups all terms according to manifestation site or etiology (e.g. infections) into 26 categories. The HLT level is the most specific aggregation level that groups phenotypic features based upon anatomy, pathology, physiology, etiology or function. As depicted in Figure 2A, the mappings of the phenotypic features to the SOC level are used to derive the organ system distribution plots as well as the organ system heterogeneity value. If desired, the user can inspect the more specific phenotype information at the HLT level in relation to the organ system distribution. These distribution plots are shown in the website along with the number of the annotated phenotypic features (Figure 2B).

Bottom Line: Some perturbations impair relatively few organ systems while others lead to highly heterogeneous or systemic effects.For perturbations of interest, the database displays the distribution of phenotypic effects across organ systems along with the heterogeneity value and the distance between organ system distributions.The Organ System Heterogeneity DB is thus a platform for the visualization and comparison of organ system level phenotypic effects of drugs, diseases and genes.

View Article: PubMed Central - PubMed

Affiliation: German Center for Diabetes Research, Neuherberg 85764, Germany Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany.

Show MeSH
Related in: MedlinePlus