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Mouse Resource Browser--a database of mouse databases

M. Zouberakis, C. Chandras, M. Swertz, D. Smedley, M. Gruenberger, J. Bard, K. Schughart, N. Rosenthal, J. M. Hancock, P. N. Schofield, G. Kollias, V. Aidinis
2010 Database: The Journal of Biological Databases and Curation  
Conflict of interest. None declared.  ...  In this context, we describe the Mouse Resource Browser (MRB; http://bioit.fleming .gr/mrb), a database of mouse databases created with the help of the European Commission framework programs MUGEN (Animal  ...  .), 16% of resources have their data accessed via a web browser interface and public data dumps, while the remaining 32% of databases allow data access simply on web Browser access (A).  ... 
doi:10.1093/database/baq010 pmid:20627861 pmcid:PMC2911845 fatcat:5yex4byp7vandlgsktsnabkioi

Pathbase: a database of mutant mouse pathology

P. N. Schofield
2004 Nucleic Acids Research  
The database interface is designed to have optimal browser and platform compatibility and to interact directly with other web-based mouse genetic resources.  ...  The database is structured around a novel ontology of mouse disorders (MPATH) and provides high-resolution downloadable images of normal and diseased tissues that are searchable through orthogonal ontologies  ...  ACKNOWLEDGEMENTS The authors would like to thank Dr Jerry Ward and Dr Janan Eppig for their support during the development of Pathbase.  ... 
doi:10.1093/nar/gkh124 pmid:14681470 pmcid:PMC308858 fatcat:cyugs34k6nfnlbulq3tznmtcji

DBTMEE: a database of transcriptome in mouse early embryos

Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi, Kenta Nakai
2014 Nucleic Acids Research  
DBTMEE (http://dbtmee.hgc.jp/) is a searchable and browsable database designed to manipulate gene expression information from our ultralarge-scale whole-transcriptome analysis of mouse early embryos.  ...  To do so, we combined the gene expression profile with various public resources.  ...  The database was developed on the supercomputer system at Human Genome Center, The Institute of Medical Science, The University of Tokyo.  ... 
doi:10.1093/nar/gku1001 pmid:25336621 pmcid:PMC4383872 fatcat:r3khr7a4gnduveidxbmcs7464m

microPIR2: a comprehensive database for human-mouse comparative study of microRNA-promoter interactions

J. Piriyapongsa, C. Bootchai, C. Ngamphiw, S. Tongsima
2014 Database: The Journal of Biological Databases and Curation  
In addition to being a reference database, microPIR2 is a tool for comparative analysis of target sites on the promoters of human-mouse orthologous genes.  ...  ., et al. microPIR2: a comprehensive database for human-mouse comparative study of microRNA-promoter interactions.  ...  on the web/database server, and open for public access.  ... 
doi:10.1093/database/bau115 pmid:25425035 pmcid:PMC4243271 fatcat:mibsz4lgyzenrjj3pn525m77wy

Mouse Resource Browser--a database of mouse databases

Michael Zouberakis, Christina Chandras, Morris Swertz, Damian Smedley, Michael Gruenberger, Jonathan Bard, Klaus Schughart, Nadia Rosenthal, John M Hancock, Paul Schofield, George Kollias, Vassilis Aidinis (+2 others)
2019
Conflict of interest. None declared.  ...  In this context, we describe the Mouse Resource Browser (MRB; http://bioit.fleming .gr/mrb), a database of mouse databases created with the help of the European Commission framework programs MUGEN (Animal  ...  .), 16% of resources have their data accessed via a web browser interface and public data dumps, while the remaining 32% of databases allow data access simply on web Browser access (A).  ... 
doi:10.17863/cam.36995 fatcat:iobfqpgcvbakbegwdjrzgm352m

dbSUPER: a database of super-enhancers in mouse and human genome [article]

Aziz Khan, Xuegong Zhang
2015 bioRxiv   pre-print
We developed dbSUPER (http://bioinfo.au.tsinghua.edu.cn/dbsuper/), the first integrated and interactive database of super-enhancers, with the primary goal of providing a resource for assistance in further  ...  We believe dbSUPER is a valuable resource for the biologists and genetic research communities.  ...  Richard Young at Whitehead Institute for Biomedical Research, MIT, for his useful suggestions and comments about the database and also sharing the data produced by his research lab, and thank for the anonymous  ... 
doi:10.1101/014803 fatcat:7uu6b5uaunhfhmdluaa6trupwu

The mouse-human anatomy ontology mapping project

T. F. Hayamizu, S. de Coronado, G. Fragoso, N. Sioutos, J. A. Kadin, M. Ringwald
2012 Database: The Journal of Biological Databases and Curation  
Conflict of interest. None declared.  ...  MA terms and identifiers are now being used by a number of database resources in descriptions of gene expression patterns and other biological data pertinent to mouse anatomy, including GXD, Pathbase (  ...  Terms from the MA ontology are currently being used by a number of database resources to describe and integrate biological information about the mouse pertinent to anatomy such as gene expression, biological  ... 
doi:10.1093/database/bar066 pmid:22434834 pmcid:PMC3308156 fatcat:mtjetnxv4jcuxoay7beregj3ze

CGDSNPdb: a database resource for error-checked and imputed mouse SNPs

Lucie N. Hutchins, Yueming Ding, Jin P. Szatkiewicz, Randy Von Smith, Hyuna Yang, Fernando Pardo-Manuel de Villena, Gary A. Churchill, Joel H. Graber
2010 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors thank Carol Bult and three anonymous referees for critical review of the manuscript. .....................................................................................  ...  Future growth of the database will be targeted primarily at large-scale projects such as the 'mouse genomes project' (http://www.sanger.ac.uk/resources/mouse/ genomes/) as well as data sets that can increase  ...  CGDSNPdb was constructed primarily as a resource to support the imputation and mouse diversity array projects, however, it is being made available as a somewhat reduced size, but high confidence, collection  ... 
doi:10.1093/database/baq008 pmid:20624716 pmcid:PMC2911843 fatcat:uuyahjxrszfulmbehmzlvlltqa

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes

A. Boccia
2004 Nucleic Acids Research  
A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts.  ...  CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp.  ...  A. Boccia was also supported by BioGeM for this project.  ... 
doi:10.1093/nar/gki011 pmid:15608249 pmcid:PMC539965 fatcat:vuigwkec55fppiiniutxqhe564

ENdb: a manually curated database of experimentally supported enhancers for human and mouse

2019 Nucleic Acids Research  
Here, we established a comprehensive manually-curated enhancer database for human and mouse, which provides a resource for experimentally supported enhancers, and to annotate the detailed information of  ...  Therefore, it is highly desirable to construct a comprehensive resource of manually curated enhancers and their related information based on low-throughput experimental evidences.  ...  For example, the VISTA Enhancer Browser (34) is a central resource for experimentally-validated human and mouse fragments with gene enhancer activity assessed in transgenic mice.  ... 
doi:10.1093/nar/gkz973 pmid:31665430 pmcid:PMC7145688 fatcat:7mvdzd5v2fe5bkuzlazujivamq

LnChrom: a resource of experimentally validated lncRNA–chromatin interactions in human and mouse

Fulong Yu, Guanxiong Zhang, Aiai Shi, Jing Hu, Feng Li, Xinxin Zhang, Yan Zhang, Jian Huang, Yun Xiao, Xia Li, Shujun Cheng
2018 Database: The Journal of Biological Databases and Curation  
Conflict of interest. None declared.  ...  A browser view has been made available as an expandable tree, and the user can easily browse all of the interaction pairs in human and mouse by 'lncRNAs', 'chromatin-modifying factors' or 'epigenetic marks  ...  A local installation of the UCSC genome browser hosted on our server is used to visualize the relevant annotations of the lncRNA binding sites on a locus-by-locus basis (29) .  ... 
doi:10.1093/database/bay039 pmid:29788225 pmcid:PMC5960994 fatcat:ssatemenk5enrp5npxsqj7fxly

MetaTropismDB: a database of organ-specific metastasis induced by human cancer cell lines in mouse models

Matteo Giulietti, Marco Bastianoni, Monia Cecati, Annamaria Ruzzo, Massimo Bracci, Marco Malavolta, Francesco Piacenza, Robertina Giacconi, Francesco Piva
2020 Database: The Journal of Biological Databases and Curation  
We created MetaTropismDB, a freely available database collecting hand-curated data useful to highlight the mechanisms of organ-specific metastasis.  ...  The organotropism is the propensity of metastatic cancer cells to colonize preferably certain distant organs, resulting in a non-random distribution of metastases.  ...  MetaTropismDB supports all major browsers are supported.  ... 
doi:10.1093/database/baaa100 pmid:33238004 fatcat:tne5twhwjvdnrd7aitlcrdqebq

dbSUPER: a database of super-enhancers in mouse and human genome

Aziz Khan, Xuegong Zhang
2015 Nucleic Acids Research  
We developed dbSUPER (http://bioinfo.au. tsinghua.edu.cn/dbsuper/), the first integrated and interactive database of super-enhancers, with the primary goal of providing a resource for assistance in further  ...  However, a centralized resource to integrate all these findings is not currently available.  ...  ACKNOWLEDGEMENTS We would like to thank Richard Young at Whitehead Institute for Biomedical Research, MIT, for his useful suggestions and comments about the database and also sharing the data produced  ... 
doi:10.1093/nar/gkv1002 pmid:26438538 pmcid:PMC4702767 fatcat:mw6kriacnnes5ch3cvgsg2llpm

The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

J. T. Eppig, J. A. Blake, C. J. Bult, J. A. Kadin, J. E. Richardson
2011 Nucleic Acids Research  
INTRODUCTION The Mouse Genome Database (MGD) (1-3) serves as a primary resource for mammalian biologists, delivering a spectrum of genetic, genomic and biological data supporting the use of mouse as a  ...  A summary of the current contents of MGD is given in Table 1 . Integrated with MGD are other components of the Mouse Genome Informatics (MGI) database resource (http://www.informatics.jax.org).  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr974 pmid:22075990 pmcid:PMC3245042 fatcat:266dcvh3yrhspdtm6q2jd3es3a
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