Analysis of disease-associated objects at the Rat Genome Database
The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. In addition to organizing biological data from rats, the RGD team focuses on manual curation of gene-disease associations for rat, human and mouse. In this work, w...
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Published in | Database : the journal of biological databases and curation Vol. 2013; p. bat046 |
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Main Authors | , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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England
Oxford University Press
2013
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Abstract | The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. In addition to organizing biological data from rats, the RGD team focuses on manual curation of gene-disease associations for rat, human and mouse. In this work, we have analyzed disease-associated strains, quantitative trait loci (QTL) and genes from rats. These disease objects form the basis for seven disease portals. Among disease portals, the cardiovascular disease and obesity/metabolic syndrome portals have the highest number of rat strains and QTL. These two portals share 398 rat QTL, and these shared QTL are highly concentrated on rat chromosomes 1 and 2. For disease-associated genes, we performed gene ontology (GO) enrichment analysis across portals using RatMine enrichment widgets. Fifteen GO terms, five from each GO aspect, were selected to profile enrichment patterns of each portal. Of the selected biological process (BP) terms, 'regulation of programmed cell death' was the top enriched term across all disease portals except in the obesity/metabolic syndrome portal where 'lipid metabolic process' was the most enriched term. 'Cytosol' and 'nucleus' were common cellular component (CC) annotations for disease genes, but only the cancer portal genes were highly enriched with 'nucleus' annotations. Similar enrichment patterns were observed in a parallel analysis using the DAVID functional annotation tool. The relationship between the preselected 15 GO terms and disease terms was examined reciprocally by retrieving rat genes annotated with these preselected terms. The individual GO term-annotated gene list showed enrichment in physiologically related diseases. For example, the 'regulation of blood pressure' genes were enriched with cardiovascular disease annotations, and the 'lipid metabolic process' genes with obesity annotations. Furthermore, we were able to enhance enrichment of neurological diseases by combining 'G-protein coupled receptor binding' annotated genes with 'protein kinase binding' annotated genes. Database URL: http://rgd.mcw.edu |
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AbstractList | The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. In addition to organizing biological data from rats, the RGD team focuses on manual curation of gene-disease associations for rat, human and mouse. In this work, we have analyzed disease-associated strains, quantitative trait loci (QTL) and genes from rats. These disease objects form the basis for seven disease portals. Among disease portals, the cardiovascular disease and obesity/metabolic syndrome portals have the highest number of rat strains and QTL. These two portals share 398 rat QTL, and these shared QTL are highly concentrated on rat chromosomes 1 and 2. For disease-associated genes, we performed gene ontology (GO) enrichment analysis across portals using RatMine enrichment widgets. Fifteen GO terms, five from each GO aspect, were selected to profile enrichment patterns of each portal. Of the selected biological process (BP) terms, 'regulation of programmed cell death' was the top enriched term across all disease portals except in the obesity/metabolic syndrome portal where 'lipid metabolic process' was the most enriched term. 'Cytosol' and 'nucleus' were common cellular component (CC) annotations for disease genes, but only the cancer portal genes were highly enriched with 'nucleus' annotations. Similar enrichment patterns were observed in a parallel analysis using the DAVID functional annotation tool. The relationship between the preselected 15 GO terms and disease terms was examined reciprocally by retrieving rat genes annotated with these preselected terms. The individual GO term-annotated gene list showed enrichment in physiologically related diseases. For example, the 'regulation of blood pressure' genes were enriched with cardiovascular disease annotations, and the 'lipid metabolic process' genes with obesity annotations. Furthermore, we were able to enhance enrichment of neurological diseases by combining 'G-protein coupled receptor binding' annotated genes with 'protein kinase binding' annotated genes. Database URL: http://rgd.mcw.edu The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus . In addition to organizing biological data from rats, the RGD team focuses on manual curation of gene–disease associations for rat, human and mouse. In this work, we have analyzed disease-associated strains, quantitative trait loci (QTL) and genes from rats. These disease objects form the basis for seven disease portals. Among disease portals, the cardiovascular disease and obesity/metabolic syndrome portals have the highest number of rat strains and QTL. These two portals share 398 rat QTL, and these shared QTL are highly concentrated on rat chromosomes 1 and 2. For disease-associated genes, we performed gene ontology (GO) enrichment analysis across portals using RatMine enrichment widgets. Fifteen GO terms, five from each GO aspect, were selected to profile enrichment patterns of each portal. Of the selected biological process (BP) terms, ‘regulation of programmed cell death’ was the top enriched term across all disease portals except in the obesity/metabolic syndrome portal where ‘lipid metabolic process’ was the most enriched term. ‘Cytosol’ and ‘nucleus’ were common cellular component (CC) annotations for disease genes, but only the cancer portal genes were highly enriched with ‘nucleus’ annotations. Similar enrichment patterns were observed in a parallel analysis using the DAVID functional annotation tool. The relationship between the preselected 15 GO terms and disease terms was examined reciprocally by retrieving rat genes annotated with these preselected terms. The individual GO term–annotated gene list showed enrichment in physiologically related diseases. For example, the ‘regulation of blood pressure’ genes were enriched with cardiovascular disease annotations, and the ‘lipid metabolic process’ genes with obesity annotations. Furthermore, we were able to enhance enrichment of neurological diseases by combining ‘G-protein coupled receptor binding’ annotated genes with ‘protein kinase binding’ annotated genes. Database URL: http://rgd.mcw.edu |
Author | Shimoyama, Mary Worthey, Elizabeth A Hayman, G T Smith, Jennifer R Jacob, Howard J Wang, Shur-Jen Laulederkind, Stanley J F Petri, Victoria Dwinell, Melinda R Munzenmaier, Diane H Nigam, Rajni Lowry, Timothy F |
AuthorAffiliation | 1 Rat Genome Database, Human and Molecular Genetics Center, 2 Department of Physiology, 3 Department of Pediatrics and 4 Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA |
AuthorAffiliation_xml | – name: 1 Rat Genome Database, Human and Molecular Genetics Center, 2 Department of Physiology, 3 Department of Pediatrics and 4 Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA |
Author_xml | – sequence: 1 givenname: Shur-Jen surname: Wang fullname: Wang, Shur-Jen email: sjwang@mcw.edu organization: Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA. sjwang@mcw.edu – sequence: 2 givenname: Stanley J F surname: Laulederkind fullname: Laulederkind, Stanley J F – sequence: 3 givenname: G T surname: Hayman fullname: Hayman, G T – sequence: 4 givenname: Jennifer R surname: Smith fullname: Smith, Jennifer R – sequence: 5 givenname: Victoria surname: Petri fullname: Petri, Victoria – sequence: 6 givenname: Timothy F surname: Lowry fullname: Lowry, Timothy F – sequence: 7 givenname: Rajni surname: Nigam fullname: Nigam, Rajni – sequence: 8 givenname: Melinda R surname: Dwinell fullname: Dwinell, Melinda R – sequence: 9 givenname: Elizabeth A surname: Worthey fullname: Worthey, Elizabeth A – sequence: 10 givenname: Diane H surname: Munzenmaier fullname: Munzenmaier, Diane H – sequence: 11 givenname: Mary surname: Shimoyama fullname: Shimoyama, Mary – sequence: 12 givenname: Howard J surname: Jacob fullname: Jacob, Howard J |
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Snippet | The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. In addition to... The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus . In addition to... |
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StartPage | bat046 |
SubjectTerms | Animals Cardiovascular Diseases - genetics Chromosomes, Mammalian - genetics Databases, Genetic Disease - genetics Genetic Association Studies Genetic Predisposition to Disease Genome - genetics Humans Mice Molecular Sequence Annotation Nervous System Diseases - genetics Obesity - genetics Original Quantitative Trait Loci - genetics Rats Software |
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Title | Analysis of disease-associated objects at the Rat Genome Database |
URI | https://www.ncbi.nlm.nih.gov/pubmed/23794737 https://search.proquest.com/docview/1371267844 https://pubmed.ncbi.nlm.nih.gov/PMC3689439 |
Volume | 2013 |
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