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. 2015 Jan 28:2015:bau128.
doi: 10.1093/database/bau128. Print 2015.

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease

Shur-Jen Wang  1 , Stanley J F Laulederkind  2 , G Thomas Hayman  2 , Victoria Petri  2 , Weisong Liu  2 , Jennifer R Smith  2 , Rajni Nigam  2 , Melinda R Dwinell  2 , Mary Shimoyama  3
Affiliations

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease

Shur-Jen Wang et al. Database (Oxford). .

Abstract

Rats have been used extensively as animal models to study physiological and pathological processes involved in human diseases. Numerous rat strains have been selectively bred for certain biological traits related to specific medical interests. Recently, the Rat Genome Database (http://rgd.mcw.edu) has initiated the PhenoMiner project to integrate quantitative phenotype data from the PhysGen Program for Genomic Applications and the National BioResource Project in Japan as well as manual annotations from biomedical literature. PhenoMiner, the search engine for these integrated phenotype data, facilitates mining of data sets across studies by searching the database with a combination of terms from four different ontologies/vocabularies (Rat Strain Ontology, Clinical Measurement Ontology, Measurement Method Ontology and Experimental Condition Ontology). In this study, salt-induced hypertension was used as a model to retrieve blood pressure records of Brown Norway, Fawn-Hooded Hypertensive (FHH) and Dahl salt-sensitive (SS) rat strains. The records from these three strains served as a basis for comparing records from consomic/congenic/mutant offspring derived from them. We examined the cardiovascular and renal phenotypes of consomics derived from FHH and SS, and of SS congenics and mutants. The availability of quantitative records across laboratories in one database, such as these provided by PhenoMiner, can empower researchers to make the best use of publicly available data. Database URL: http://rgd.mcw.edu.

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Figures

Figure 1.
Figure 1.
(A) Final search page before generating a report in PhenoMiner. A total of 18 records were retrieved by limiting data to four ontologies: Rat Strain, Clinical Measurement, Measurement Method and Experimental Condition. The record distribution in each ontology is shown in parentheses following the term. (B) Chart display of MAP data set generated in PhenoMiner. These records are from SS/Jr (RGD: 10041) on controlled sodium content diets: low, 2%, or 8%. Each bar represents one experiment and the experimental conditions and measurement methods associated with the experiment are color coded and explained under “Conditions and Measurement Methods.” To simplify the display, these experimental details of each bar are omitted. (Data accessed June 2014)
Figure 2.
Figure 2.
Effect of diet sources on MAP in four rat strains: BN, FHH, SHR and SS. Top: MAP was measured in rats on 0.4% salt-containing chows from Dyets or Teklad. Bottom: MAP was measured in rats on 4% salt-containing chows from Dyets or Teklad. Data for each strain were downloaded from PhenoMiner. The official nomenclature for the rat strains shown are BN/NHsdMcwi (BN), FHH/EurMcwi (FHH), SHR/NCrl (SHR) and SS/JrHsdMcwi (SS). Data tables underneath the charts show the mean values of each group. *P < 0.05 vs. same strain on Dyets chow.
Figure 3.
Figure 3.
(A) SBP of SS.LEW congenic rats from PhenoMiner. Black horizontal bars indicate congenics that had comparable SBP to the parents and blue horizontal bars indicate congenics that had lower SBP than the parents. (B) MAP of SS chromosome 1 mutants from PhenoMiner. −\−, homozygous mutant; −\+, heterozygous mutant; +\+, wild-type control.
Figure 4.
Figure 4.
Scatterplots of daily UPE and MAP in SS mutants and wild-type controls on a 4% salt diet. Each data point is the average for a rat strain. Details are downloadable from the expanded data tables in PhenoMiner.
See this image and copyright information in PMC

References

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