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The Rat Genome Database 2009: variation, ontologies and pathways

by Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-gungor, Jeffrey Depons, Stanley Laulederkind, Timothy Lowry, Rajni Nigram, Simon N. Twigger, Howard J. Jacob, The Rgd Team - Nucleic Acids Res , 2009
"... gies and pathways ..."
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gies and pathways

doi:10.1093/nar/gkn842 The Rat Genome Database 2009: variation, ontologies and pathways

by Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-gungor, Jeffrey Depons, Stanley Laulederkind, Timothy Lowry, Rajni Nigram, Simon N. Twigger, Howard J. Jacob, The Rgd Team , 2008
"... The Rat Genome Database (RGD, ..."
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The Rat Genome Database (RGD,

Original Article Ontology searching and browsing at the Rat Genome Database

by Stanley J. F. Laulederkind, Marek Tutaj, Mary Shimoyama, G. Thomas Hayman, Timothy F. Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-jen Wang, Jeff De Pons, Melinda R. Dwinell, Howard J. Jacob
"... The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40 000 rat gene records, as well as human and mouse orthologs, 1857 rat and 1912 human quantitative trait loci (QTLs) and 2347 rat strains. Biological information curated for these data ..."
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The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40 000 rat gene records, as well as human and mouse orthologs, 1857 rat and 1912 human quantitative trait loci (QTLs) and 2347 rat strains. Biological information curated for these data

Original article PhenoMiner: quantitative phenotype curation at the rat genome database

by Stanley J. F. Laulederkind, Weisong Liu, Jennifer R. Smith, G. Thomas Hayman, Shur-jen Wang, Rajni Nigam, Victoria Petri, Timothy F. Lowry, Jeff De Pons, Melinda R. Dwinell, Mary Shimoyama
"... The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses>40 000 rat gene records as well as human and mouse orthologs,>2000 rat and 1900 human quantitative trait loci (QTLs) records and>2900 rat strain records. Biological information curat ..."
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The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses>40 000 rat gene records as well as human and mouse orthologs,>2000 rat and 1900 human quantitative trait loci (QTLs) records and>2900 rat strain records. Biological information

Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

by Sara C. Novais, Joel Arrais, Pedro Lopes, Tine V, Wim De Coen, Dick Roelofs, Amadeu M. V. M. Soares, Mónica J. B. Amorim
"... Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can ..."
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and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From

RESEARCH ARTICLE Endoplasmic Reticulum Stress in Heat- and Shake-Induced Injury in the Rat Small Intestine

by Peng Yin, Jianqin Xu, Shasha He, Fenghua Liu, Jie Yin, Yulong Yin, Xiaolong Xu, Zhaofei Xia
"... We investigated the mechanisms underlying damage to rat small intestine in heat- and shake-induced stress. Eighteen Sprague-Dawley rats were randomly divided into a control group and a 3-day stressed group treated 2 h daily for 3 days on a rotary platform at 35°C and 60 r/min. Hematoxylin and eosin- ..."
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We investigated the mechanisms underlying damage to rat small intestine in heat- and shake-induced stress. Eighteen Sprague-Dawley rats were randomly divided into a control group and a 3-day stressed group treated 2 h daily for 3 days on a rotary platform at 35°C and 60 r/min. Hematoxylin and eosin

EMBnet.journal 18.B PostErs 151 A first RDF implementation of the COSMIC database on mutations in cancer

by Paolo Romano
"... Within a living organism, genome and proteome variations may influence many molecular inter-actions and biochemical pathways, leading to deleterious effects in the proper activity of cells, tissues, and organs; ultimately, this may be the cause of many syndromes and diseases. It is now well known th ..."
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Within a living organism, genome and proteome variations may influence many molecular inter-actions and biochemical pathways, leading to deleterious effects in the proper activity of cells, tissues, and organs; ultimately, this may be the cause of many syndromes and diseases. It is now well known

BIOMEDICAL SEMANTICS

by Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G Thomas Hayman, Jennifer R Smith, Jeff De Pons, Shur-jen Wang, Mary Shimoyama
"... Background: The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hierarchical structure of a directed acyclic graph. The ontology allows for the sta ..."
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Background: The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hierarchical structure of a directed acyclic graph. The ontology allows

Transcriptome Analysis of the Hippocampus in Novel Rat Model of Febrile Seizures

by Zhongcheng Wang, Yuanteng Fan, Jian Xu, Liang Li, Duanhe Heng, Song Han, Jun Yin, Biwen Peng Wanhong Liu
"... Febrile seizures (FS) are the most common type of convulsive events in infants and young children, but the precise underlying genetic mechanism remains to be explored. To investigate the underlying pathogenic factors in FS and subsequent epilepsy, alterations in gene expression between the two new s ..."
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strains of rats (hyperthermia-prone [HP] vs hyperthermia-resistant [HR]), were investigated by using the Whole Rat Genome Oligo Microarray. This process identified 1,140 differentially expressed genes (DEGs; 602 upregulated and 538 downregulated), which were analyzed to determine significant Gene Ontology

doi:10.1155/2012/695898 Research Article Global Gene Expression Profiling in PPAR-γ Agonist-Treated Kidneys in an Orthologous Rat Model of

by Human Autosomal, Recessive Polycystic, Kidney Disease
"... Copyright © 2012 Daisuke Yoshihara et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Kidneys are enlarged by aberrant proliferat ..."
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pathways identified to be downregulated by PIOtreatment were related to cell cycle and proliferation, including EGF, PDGF and JNK pathways. Their relevant pathways were identified using the Kyoto Encyclopedia of Gene and Genomes database. Stearoyl-
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