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ORegAnno Citation

CITATION

Montgomery S.B.*, Griffith O.L.*, Sleumer M.C., Bergman C.M., Bilenky M., Pleasance E.D., Prychyna Y., Zhang X., Jones S.J.M. "ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation", Bioinformatics, March 2006. *These authors contributed equally to this work.

In cases where ORegAnno acts as a proxy to datasets originally stored in other collections (listed below or from individual records), these authors should be explicitly cited (either in conjunction with or in lieu of ORegAnno). Our web services will soon provide this information with returned results as to appropriate citation information for incorporated datasets within ORegAnno.

ACKNOWLEDGEMENTS

This project was funded by Genome Canada, the Michael Smith Foundation for Health Research, the Natural Sciences and Engineering Research Council, and the Canadian Insititute for Health Research. It will received ongoing maintenance and support from 2005 through 2007. Data collaborations are being actively pursued; a list of currently integrated datasets is listed below.

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MAJOR CONTRIBUTORS

Resource

Contribution and notes

Reference

URL

REDfly database, Buffalo University, U.S.A.

CRMs annotated from literature for Drosophila melanogaster

Gallo, Li, Hu, Halfon (2006)

REDfly database

Claes Wadelius, Department of Genetics & Pathology, Uppsala University, Sweden

Records were contributed for HNF-3beta, HNF-4alpha, USF1 and C/EBP sites

N/A

Department of Genetics and Pathology

Stanford ENCODE Promoter Set

Promoters identified in multiple cell lines from Rick Myer's group at Stanford. This set includes more cell lines than in the original publication.

Trinklein, Aldred, Saldanha, Myers (2003)

Myer's Lab

Drosophila DNase I Footprint Database (v2.0)

1330 Drosophila DNase I footprint sites. The complete data set was obtained from www.flyreg.org. Every record in ORegAnno from this resource includes the url and FPID as a comment.

Bergman, Carlson and Celniker (2005)

www.flyreg.org

Wasserman, Fickett et al. Muscle/Liver set

A large number of sites were obtained from a muscle/liver-specific set.

Wasserman and Fickett (1998); Ho Sui et al. (2005)

www.cbil.upenn.edu/MTIR/TOC.html; www.cisreg.ca/tjkwon/

rSNP_guide

A number of rSNP_guide rSNP records were included after manual verification against literature. Currently, only those reported as natural variation are included.

Ponomarenko et al (2003)

wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/

Efimenko et al (2005) Analysis of xbx genes in C. elegans

A total of 8 sites were obtained from a list curated by Efimenko et al (2005)

Efimenko et al (2005)

N/A
 

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