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4DXpress: a database for cross-species expression pattern comparisons

Y. Haudry, H. Berube, I. Letunic, P.-D. Weeber, J. Gagneur, C. Girardot, M. Kapushesky, D. Arendt, P. Bork, A. Brazma, E. E. M. Furlong, J. Wittbrodt (+1 others)
2007 Nucleic Acids Research  
Therefore, we have integrated expression patterns for zebrafish, Drosophila, medaka and mouse into a central public repository called 4DXpress (expression database in four dimensions).  ...  In these species, expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for Drosophila  ...  ACKNOWLEDGEMENTS This work was carried out in the Centre for Computational Biology at EMBL. We are grateful to the model organism database crews for providing us their expression pattern data.  ... 
doi:10.1093/nar/gkm797 pmid:17916571 pmcid:PMC2238840 fatcat:4zmk4eyxsfgmpja4lv4aubjr5u

COMPARING AND ANALYSING GENE EXPRESSION PATTERNS ACROSS ANIMAL SPECIES USING 4DXPRESS

YANNICK HAUDRY, CHUANG KEE ONG, LAURENCE ETTWILLER, HUGO BERUBE, IVICA LETUNIC, MISHA KAPUSHESKY, PAUL-DANIEL WEEBER, XI WANG, JULIEN GAGNEUR, CHARLES GIRARDOT, DETLEV ARENDT, PEER BORK (+4 others)
2007 Proceedings of the 6th Asia-Pacific Bioinformatics Conference  
Expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for drosophila or MGI for mouse.  ...  For this purpose we have integrated gene expression data for zebrafish, medaka, drosophila and mouse into a central public repository named 4DXpress (http://ani.embl.de/4DXpress). 4DXpress allows to query  ...  Acknowledgement This work was carried out in the Centre for Computational Biology at EMBL. We are grateful to the model organism database crews for providing us their expression pattern data.  ... 
doi:10.1142/9781848161092_0038 fatcat:4wxmalyhhvhlfcxqcehozebnfa

Understanding Kidney Disease: Toward the Integration of Regulatory Networks Across Species

Wenjun Ju, Frank C. Brosius
2010 Seminars in Nephrology  
in targeted identification of regulatory networks that may have clinical relevance for human kidney diseases.  ...  Systems biology provides a relatively new set of approaches to identify similarities and differences between animal models and humans that may lead to a more comprehensive understanding of human kidney  ...  Acknowledgments We thank Viji Nair, Celine Berthier, Markus Bitzer, Felix Eichinger, Sebastian Martini and Subramaniam Pennathur for insightful discussion and critical reading of the manuscript.  ... 
doi:10.1016/j.semnephrol.2010.07.008 pmid:21044762 pmcid:PMC2989742 fatcat:7elrkoc7c5f3di5plisdh2l26a

Integrating human and murine anatomical gene expression data for improved comparisons

Natalia Jiménez-Lozano, Joan Segura, José Ramón Macías, Juanjo Vega, José María Carazo
2011 Computer applications in the biosciences : CABIOS  
Motivation: Information concerning the gene expression pattern in four dimensions (species, genes, anatomy and developmental stage) is crucial for unraveling the roles of genes through time.  ...  There are a variety of anatomical gene expression databases, but extracting information from them can be hampered by their diversity and heterogeneity.  ...  We sincerely thank the staff of EMAGE, GXD, GENSAT, ABA, KEGG, BioGPS, Human Protein Atlas, EUREXPRESS and the OMIM databases for free data base access and maintenance, and particularly Susan Lindsay for  ... 
doi:10.1093/bioinformatics/btr639 pmid:22106336 fatcat:t7fqcfmqrrhifofblee6jvivoy

A comparative gene expression database for invertebrates

Mattias Ormestad, Mark Q Martindale, Eric Röttinger
2011 EvoDevo  
for invertebrates that allows species-specific as well as cross-species gene expression comparisons.  ...  Conclusions: This database provides a unique tool for the Evo-Devo research community that allows the retrieval, analysis and comparison of gene expression patterns within or among species.  ...  Acknowledgements The authors are thankful to the members of the Martindale lab for their inputs during the development of the database and to the researchers who submitted their published and unpublished  ... 
doi:10.1186/2041-9139-2-17 pmid:21861937 pmcid:PMC3180427 fatcat:udshptfkwzfrba2hsqpojmha2a

FlyTED: the Drosophila Testis Gene Expression Database

Jun Zhao, Graham Klyne, Elizabeth Benson, Elin Gudmannsdottir, Helen White-Cooper, David Shotton
2009 Nucleic Acids Research  
FlyTED, the Drosophila Testis Gene Expression Database, is a biological research database for gene expression images from the testis of the fruit fly Drosophila melanogaster.  ...  It currently contains 2762 mRNA in situ hybridization images and ancillary metadata revealing the patterns of gene expression of 817 Drosophila genes in testes of wild type flies and of seven meiotic arrest  ...  One of our aims has been to determine the expression patterns for genes that require the meiotic arrest genes for their expression, in comparison with those whose expression in testes is independent of  ... 
doi:10.1093/nar/gkp1006 pmid:19934263 pmcid:PMC2808924 fatcat:h6ecgitkkzbath5py75f6idk4m

More than a decade of developmental gene expression atlases: where are we now?

Bouke A. de Boer, Jan M. Ruijter, Frans P. J. M. Voorbraak, Antoon F. M. Moorman
2010 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors thank Arie Hasman and Maurice van den Hoff for their valuable suggestions after critically reading the manuscript and Alexandre Soufan for discussions about the 3D gene expression  ...  However, any cross-species mapping of ontologies will be a great challenge.  ...  COMPARE (35) and 4DXpress (36) are databases that combine the expression information of more than one species by importing gene expression data from the gene expression atlases that were already set  ... 
doi:10.1093/nar/gkq070 fatcat:4f3o24bb3jfyljytq6sskrcwem

More than a decade of developmental gene expression atlases: where are we now?

B. A. de Boer, J. M. Ruijter, F. P. J. M. Voorbraak, A. F. M. Moorman
2009 Nucleic Acids Research  
, both for relations as well as for anatomical terms.  ...  Our aim is to provide insights into both the possibilities of the atlases, as well as to describe what more than a decade of developmental gene expression atlases can teach us about the requirements of  ...  ACKNOWLEDGEMENTS The authors thank Arie Hasman and Maurice van den Hoff for their valuable suggestions after critically reading the manuscript and Alexandre Soufan for discussions about the 3D gene expression  ... 
doi:10.1093/nar/gkp819 pmid:19822576 pmcid:PMC2794177 fatcat:b42adqur7zd4bewbbxxzg6gjei

Combining Computational Prediction of Cis-Regulatory Elements with a New Enhancer Assay to Efficiently Label Neuronal Structures in the Medaka Fish

Emmanuel Mongin, Thomas O. Auer, Franck Bourrat, Franziska Gruhl, Ken Dewar, Mathieu Blanchette, Joachim Wittbrodt, Laurence Ettwiller, Christoph Winkler
2011 PLoS ONE  
patterns remains a limiting step.  ...  The labeling of living cells in these structures is key for the understanding of brain development and function, yet the generation of stable lines expressing reporter genes in specific spatio-temporal  ...  Acknowledgments We wish to thank Pablo Cingolani for taking care of the PReMod web site and database. We would like to thank the fish room team for fish husbandry. Author Contributions  ... 
doi:10.1371/journal.pone.0019747 pmid:21637758 pmcid:PMC3103512 fatcat:hxuzkdhsn5ah3dmwibxdez44ku

A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database

Kshitish K Acharya, Darshan S Chandrashekar, Neelima Chitturi, Hardik Shah, Varun Malhotra, Sreelakshmi KS, Deepti H, Akhilesh Bajpai, Sravanthi Davuluri, Pranami Bora, Leena Rao
2010 BMC Genomics  
To overcome such limitations, we have taken up a new strategy to predict gene expression patterns using available information, for one tissue at a time.  ...  This process resulted in a richer collection of gene expression data compared to other databases/resources, for multiple testicular conditions.  ...  ; 4DXpress: EXpression database in 4D (four dimensions).  ... 
doi:10.1186/1471-2164-11-467 pmid:20699007 pmcid:PMC3091663 fatcat:x7h6v5g7azdjlcq5nkg73eecgy

The Characterization Tool: A knowledge-based stem cell, differentiated cell, and tissue database with a web-based analysis front-end

Inken Wohlers, Harald Stachelscheid, Joeri Borstlap, Katrin Zeilinger, Jörg C. Gerlach
2009 Stem Cell Research  
It currently holds more than 7000 marker expressions for different human embryonic stem cell lines, adult stem cells, and differentiated cells. a v a i l a b l e a t w w w. s c i e n c e d i r e c t .  ...  , cross-references to other databases, text descriptions, information on characterization experiments, and image storage.  ...  We thank Alexander Damaschun for helpful discussions and critical review of the manuscript and Martin Pietsch for technical support.  ... 
doi:10.1016/j.scr.2009.05.001 pmid:19520631 fatcat:7rpylp2npjbvbgvjffda2yhkru

Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data

Michael J Gilchrist, Mikkel B Christensen, Richard Harland, Nicolas Pollet, James C Smith, Naoto Ueno, Nancy Papalopulu
2008 BMC Bioinformatics  
This provides some challenges for text based access, especially for cross-species searches.  ...  In particular the method facilitates cross-species comparisons, and enables the handling of novel or otherwise un-annotated genes.  ...  organism database, ANISEED.  ... 
doi:10.1186/1471-2105-9-442 pmid:18928517 pmcid:PMC2587480 fatcat:jkc764pnjrhg3ggxic2zogcc4y

Metadata matters: access to image data in the real world

Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco (+4 others)
2010 Journal of Cell Biology  
Alexia Ferrand for preparation of samples for structured illumination data and Angus Lamond for critical reading of the manuscript. Work on OME in J.R.  ...  http://www.fruitfly.org/cgi-bin/ex/insitu.pl Zebrafish Model Organism Database Gene expression patterns during zebrafish development http://zfin.org; Sprague et al., 2006 4DXpress Cross-species gene  ...  express pattern comparison http://4dx.embl.de/4DXpress; Haudry et al., 2008 Subcellular Localization Resource SLIF and PSLID Web-based resources for the computational determination and mining of  ... 
doi:10.1083/jcb.201004104 pmid:20513764 pmcid:PMC2878938 fatcat:ixmveesicvc6bfolxuwf32eftu

Evolutionary crossroads in developmental biology: annelids

D. E. K. Ferrier
2012 Development  
Annelids (the segmented worms) have a long history in studies of animal developmental biology, particularly with regards to their cleavage patterns during early development and their neurobiology.  ...  With the relatively recent reorganisation of the phylogeny of the animal kingdom, and the distinction of the super-phyla Ecdysozoa and Lophotrochozoa, an extra stimulus for studying this phylum has arisen  ...  Detlev Arendt is thanked for first drawing the author's attention to the Nietzsche quote used at the start of this article.  ... 
doi:10.1242/dev.074724 pmid:22782719 fatcat:t2cwr4m2jzepnhs4t3ibjd6g74