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ORegAnno: an open-access community-driven resource for regulatory annotation

O. L. Griffith, S. B. Montgomery, B. Bernier, B. Chu, K. Kasaian, S. Aerts, S. Mahony, M. C. Sleumer, M. Bilenky, M. Haeussler, M. Griffith, S. M. Gallo (+17 others)
2007 Nucleic Acids Research  
ORegAnno is an open-source, open-access database and literature curation system for communitybased annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and  ...  Users can enter or 'check out' papers from the queue for manual curation using a series of user-friendly annotation pages.  ...  ACKNOWLEDGEMENTS We thank the Open Regulatory Annotation Consortium for their continuing efforts to improve this resource through manual curation and record validation.  ... 
doi:10.1093/nar/gkm967 pmid:18006570 pmcid:PMC2239002 fatcat:a2mf7bj4hrcplodqlcmh62lroe

ORegAnno 3.0: a community-driven resource for curated regulatory annotation

Robert Lesurf, Kelsy C. Cotto, Grace Wang, Malachi Griffith, Katayoon Kasaian, Steven J. M. Jones, Stephen B. Montgomery, Obi L. Griffith
2015 Nucleic Acids Research  
.; and The Open Regulatory Annotation Consortium, ,"ORegAnno 3.0: A community-driven resource for curated regulatory annotation.  ...  ABSTRACT The Open Regulatory Annotation database (ORe-gAnno) is a resource for curated regulatory annotation.  ...  ACKNOWLEDGEMENTS We thank the Open Regulatory Annotation Consortium for their continuing contributions to ORegAnno through the identification of relevant publications and manual curation efforts.  ... 
doi:10.1093/nar/gkv1203 pmid:26578589 pmcid:PMC4702855 fatcat:cosm3gv6ungulaj2uimhexkcvm

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

M. S. Halfon, S. M. Gallo, C. M. Bergman
2007 Nucleic Acids Research  
for regulatory bioinformatics.  ...  Drosophila cis-regulatory data that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation.  ...  Funding to pay the Open Access publication charges for this article was provided by the University at Buffalo. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm876 pmid:18039705 pmcid:PMC2238825 fatcat:vyryxdivxvbltkms4qcmupxsoa

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation

Elodie Portales-Casamar, Stefan Kirov, Jonathan Lim, Stuart Lithwick, Magdalena I Swanson, Amy Ticoll, Jay Snoddy, Wyeth W Wasserman
2007 Genome Biology  
PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction.  ...  PAZAR, located at http://www.pazar.info, is open for business.  ...  Acknowledgements We acknowledge Dimas Yusuf for the drawing of the PAZAR mall map and Jerome Bacconnier for the PAZAR logo and Web interface design.  ... 
doi:10.1186/gb-2007-8-10-r207 pmid:17916232 pmcid:PMC2246282 fatcat:soa6qfusyjcefiwmv3jsnjb4z4

Text-mining assisted regulatory annotation

Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L Griffith, Paco Hulpiau, Steven JM Jones, Stephen B Montgomery, Casey M Bergman, The Open Regulatory Annotation Consortium
2008 Genome Biology  
We are especially grateful to Martin Krallinger, Lynette Hirschman, Alfonso Valencia and Ewan Birney for encouraging links between the regulatory informatics and text-mining communities.  ...  Acknowledgements We thank Jonathan Wren for help running his Markov sequence extraction method as well as all of the participants of the RegCreative Jamboree for many fruitful discussions before, during  ...  Both ORegAnno and PAZAR provide principled, standardized technologies for the long-term, community-driven, open-access annotation of cisregulatory data in the context of the major genome database resources  ... 
doi:10.1186/gb-2008-9-2-r31 pmid:18271954 pmcid:PMC2374703 fatcat:rplmnumegze4hg3kdc37tykuim

A Comparative Analysis of Bioinformation Website Services
생명정보 분야 웹사이트 서비스에 대한 비교.분석에 관한 연구

Bu-Young Ahn, Eung-Bong Lee
2009 Journal of Information Management  
Obi Griffith(2007)은 어노테이션 조정을 위한 오픈액세스 커뮤니티 주도 자원(OReg Anno: an open-access community-driven resource for regulatory annotation)에 관 한 연구에서 오픈액세스, 오픈 소스 기반의 ORegAnno를 제안하였다.  ...  ORegAnno는 DNA 조절에 관한 특정 분야에 적용되는 어노테이션 시스 템으로 생명정보 분야 웹사이트에서 서비스되 어야 하는 콘텐트의 하나가 될 수 있다. 이렇 게 전문적이고 세부적인 연구결과를 웹사이트 에서 서비스하는 콘텐트로 추가하는 작업도 중요한 일이라고 생각된다.  ... 
doi:10.1633/jim.2009.40.1.157 fatcat:7kahuuqgozdcxfitxu6a7uhjea

Public data sources for regulatory genomic features

Samuele Garda, Jana Marie Schwarz, Markus Schuelke, Ulf Leser, Dominik Seelow
2021 Medizinische Genetik  
All this information can be helpful in interpreting variants in the regulatory genome.  ...  High-throughput technologies have led to a continuously growing amount of information about regulatory features in the genome.  ...  The functional annotation of regulatory features and their description is less straightforward than for the coding DNA sequence.  ... 
doi:10.1515/medgen-2021-2075 fatcat:ekocyu66vbb7vek3k42sstv5oq

EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression

M Inmaculada Barrasa, Philippe Vaglio, Fabien Cavasino, Laurent Jacotot, Albertha J M Walhout
2007 BMC Genomics  
EDGEdb provides a protein-DNA -and protein-protein interaction resource for C. elegans transcription factors and a framework for similar databases for other organisms.  ...  We have already mapped several hundred protein-DNA interactions and analyzed the transcriptional consequences of some by examining differential gene expression of targets in the presence or absence of an  ...  Acknowledgements We thank the members of the Walhout laboratory and Job Dekker for discussion and critical reading of the manuscript, and NIDDK for funding (R01DK068429). We also thank D.  ... 
doi:10.1186/1471-2164-8-21 pmid:17233892 pmcid:PMC1790901 fatcat:liamp2b23vebhnlnvzgern4pp4

2008 EMBO Young Investigator Programme Application

Casey Bergman
2012 Figshare  
Jones &The Open Regulatory Annotation Consortium. (2007) ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research 36:D107-D113. 22) Bergman, C.M. & H.  ...  Jones (2006) ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.  ... 
doi:10.6084/m9.figshare.94127.v1 fatcat:lm4hewz2tfdxbnhtgqqn275mtq

Semantic integration of data on transcriptional regulation

Michael Baitaluk, Julia Ponomarenko
2010 Computer applications in the biosciences : CABIOS  
However, there are no resources to integrate these data automatically or to provide a 'one-stop shop' experience for users seeking information essential for deciphering and modeling gene regulatory networks  ...  Gupta for valuable discussions and assistance in creation of IntegromeDB and W. Bluhm for critical reading of the manuscript.  ...  ORegAnno (Griffith et al., 2008) is an open-source open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, TFBSs and regulatory  ... 
doi:10.1093/bioinformatics/btq231 pmid:20427517 pmcid:PMC2887046 fatcat:7g6zzhyjbzaplhqauhptunr47q

Prediction and analysis of functional RNA structures within the integrative genomics viewer

Warren B Rouse, Ryan J Andrews, Nicholas J Booher, Jibo Wang, Michael E Woodman, Ernst R Dow, Theodore C Jessop, Walter N Moss
2022 NAR Genomics and Bioinformatics  
This new tool offers the RNA community an easy to use tool to find, analyze, and characterize RNA secondary structures in the context of all available data, in order to find those worthy of further analyses  ...  This allows users to directly perform structure predictions and visualize results—in conjunction with probing data and other annotations—in one program.  ...  ACKNOWLEDGEMENTS Thank you to Levi Baber and the Iowa State University Research IT group for their support over the course of this project and members of the Moss Lab for their input. FUNDING  ... 
doi:10.1093/nargab/lqab127 pmid:35047817 pmcid:PMC8759568 fatcat:lr64kmuq5fgfjms72yx74hk2li

2008 BBSRC Tools and Resources Development Fund Application - pubmed2ensembl: a resource for linking biological literature to genome sequences

Casey Bergman, Goran Nenadic
2012 Figshare  
2008 BBSRC Tools and Resources Development Fund application. Awarded.  ...  Finally, the pubmed2ensembl resource will be open-access and open-source so as to maximise access to it by the wider research community, and to encourage use of pubmed2ensembl data or services in other  ...  with curated cis-regulatory data in the ORegAnno Database.  ... 
doi:10.6084/m9.figshare.94137.v2 fatcat:63oszpocifezhoznpqvjc4nn3i

Benchmark and integration of resources for the estimation of human transcription factor activities

Luz Garcia-Alonso, Christian H. Holland, Mahmoud M. Ibrahim, Denes Turei, Julio Saez-Rodriguez
2019 Genome Research  
We provide an integrated resource of all TF-target interactions derived through these strategies, with confidence scores, as a resource for enhanced prediction of TF activities.  ...  We assembled a collection of TF-target interactions for 1541 human TFs and evaluated how different molecular and regulatory properties of the TFs, such as the DNA-binding domain, specificities, or mode  ...  This work was supported by Open Targets (grant number OTAR016), Germany Federal Ministry of Education and Research grant "LiSyM" (FKZ 031L0041), and the JRC for Computational Biomedicine, which is partially  ... 
doi:10.1101/gr.240663.118 pmid:31340985 pmcid:PMC6673718 fatcat:oc2fyvmaf5et5gubbqgr35syae

Exploring Transcriptional Regulatory Networks in the Worm

Illés J. Farkas, Qasim K. Beg, Zoltán N. Oltvai
2006 Cell  
Using a yeast one-hybrid assay, Deplancke et al. (2006) report in this issue a protein-DNA interaction network for 72 gene promoters and 117 regulatory proteins expressed in cells of the nematode digestive  ...  This study is a first step toward mapping transcriptional regulatory networks in distinct metazoan cell lineages and organs using a "gene-centered" approach.  ...  This difficulty may be alleviated in part through community-level open access annotation projects such as ORegAnno established for transcriptional interactions (Montgomery et al., 2006) .  ... 
doi:10.1016/j.cell.2006.06.002 pmid:16777593 fatcat:u7r34fwcjvahjhjsy4cwnwweda

Integrated intra- and intercellular signaling knowledge for multicelullar omics analysis [article]

Denes Turei, Alberto Valdeolivas, Lejla Gul, Nicolas Palacio-Escat, Olga Ivanova, Attila Gabor, Dezso Modos, Tamas Korcsmaros, Julio Saez-Rodriguez
2020 bioRxiv   pre-print
The resource is available for human, and via homology translation for mouse and rat.  ...  However, knowledge of intercellular communication is scarce, scattered across different resources, and not linked to intracellular processes.  ...  Complex annotations Only four resources curate annotations of protein complexes, from these we processed the complex annotations as we did for proteins.  ... 
doi:10.1101/2020.08.03.221242 fatcat:nu6ba3h6ajg3zcf23b3zx5aezq
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