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The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments [article]

Pablo Cordero, Julius Lucks, Rhiju Das
2011 arXiv   pre-print
need for a database to enable sharing, visualization, and meta-analyses of these data.  ...  We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely  ...  Acknowledgements and Funding We thank the authors of RNAstructure, ViennaRNA, VARNA, and the Stanford Visualization Team for making their source code freely available. We also thank R.  ... 
arXiv:1110.0235v1 fatcat:bir5gpfpfrcnjoz7gblzrd4ndy

An RNA Mapping DataBase for curating RNA structure mapping experiments

Pablo Cordero, Julius B. Lucks, Rhiju Das
2012 Computer applications in the biosciences : CABIOS  
for sharing, visualization, search and meta-analysis.  ...  We have established an RNA mapping database (RMDB) to enable structural, thermodynamic and kinetic comparisons across single-nucleotide-resolution RNA structure mapping experiments.  ...  ACKNOWLEDGEMENTS We thank the authors of RNAstructure, VARNA and the Stanford Visualization Team for making their source code freely available, the Laederach laboratory for aid with SNRNASM integration  ... 
doi:10.1093/bioinformatics/bts554 pmid:22976082 pmcid:PMC3496344 fatcat:fu26yxe7h5ef3namgo3fldkc2q

Sharing and archiving nucleic acid structure mapping data

P. Rocca-Serra, S. Bellaousov, A. Birmingham, C. Chen, P. Cordero, R. Das, L. Davis-Neulander, C. D. S. Duncan, M. Halvorsen, R. Knight, N. B. Leontis, D. H. Mathews (+5 others)
2011 RNA: A publication of the RNA Society  
Supplemental http://rnajournal.cshlp.org/content/suppl/2011/05/13/rna.2753211.DC1.html References http://rnajournal.cshlp.org/content/17/7/1204.full.html#related-urls Article cited in: http://rnajournal.cshlp.org  ...  At present, there is currently no standard database for archiving and sharing nucleic acid structure mapping data, despite the compelling opportunities to incorporate such data in studies with direct relevance  ...  We used a tool to project structure mapping data on an RNA secondary structure diagram provided with the SAFA software (Das et al. 2005) to visualize the DMS data from these experiments on two-dimensional  ... 
doi:10.1261/rna.2753211 pmid:21610212 pmcid:PMC3138558 fatcat:fbs2tdppyvgornwjwwqx7rd2jy

RNA structure inference through chemical mapping after accidental or intentional mutations

Clarence Y. Cheng, Wipapat Kladwang, Joseph D. Yesselman, Rhiju Das
2017 Proceedings of the National Academy of Sciences of the United States of America  
The data were displayed in a 2D heatmap visualization analogous to that used for prior mutate-and-map experiments: a 1D chemical-mapping profile was estimated for each single-nucleotide variant in the  ...  To understand whether M2-seq signals could be enhanced for the GIR1 ribozyme and other RNAs, we carried out extensive experiments to understand the mechanism for the signal in the P4-P6 RNA, varying transcription  ...  The data were displayed in a 2D heatmap visualization analogous to that used for prior mutate-and-map experiments: a 1D chemical-mapping profile was estimated for each single-nucleotide variant in the  ... 
doi:10.1073/pnas.1619897114 pmid:28851837 pmcid:PMC5603990 fatcat:jgtlwjcvsjab7mi4tqzf6jz3ey

Web-Based Arabidopsis Functional and Structural Genomics Resources

Yan Lu, Robert L. Last
2008 The Arabidopsis Book  
ACKNOWLEDGMENTS The Chloroplast 2010 Project was supported by the National Science Foundation (grant no. MCB-0519740).  ...  One useful feature is that users can visualize protein gel images for the proteome experiments.  ...  After clicking the 'submit' button, a new window opens up, showing a list of miRNA candidates with miRNA precursor candidates and RNA fold structures, which is unique for this database.  ... 
doi:10.1199/tab.0118 pmid:22303243 pmcid:PMC3243351 fatcat:swsrfjpxszaobflnda7udjizwa

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, Georgios A. Pavlopoulos
2021 Biomolecules  
Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between  ...  To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability  ...  RNA network structures are presented as interactive graphs, where nodes depict the basic secondary structure of motifs and edges represent either shared bases or tertiary interactions.  ... 
doi:10.3390/biom11081245 pmid:34439912 pmcid:PMC8391349 fatcat:32aums2jtbc5vdcdknzfczajsy

Correcting a SHAPE-directed RNA structure by a mutate-map-rescue approach [article]

Siqi Tian, Pablo Cordero, Wipapat Kladwang, Rhiju Das
2014 bioRxiv   pre-print
These results correct an erroneous SHAPE inference of a ribosomal conformational change and suggest a general mutate-map-rescue approach for dissecting RNA dynamic structure landscapes.  ...  Computational support estimates, data from alternative chemical probes, and mutate-and-map (M2) experiments expose limitations of prior methodology and instead give a near-crystallographic secondary structure  ...  Data Reposition All chemical mapping datasets, including one-dimensional mapping, mutate-and-map, and mutation/rescue, have been deposited at the RNA Mapping Database (http://rmdb.stanford.edu) (Cordero  ... 
doi:10.1101/001966 fatcat:yojo5r7iw5ckbfka7l324peiwq

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Peter B. Becker
2011 PLoS Biology  
Data and derived results are made available through a freely accessible database.  ...  The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and  ...  Wexler and Julia Zhang at the National Human Genome Research Institute for their support in administering the ENCODE Consortium, additional members of our laboratories and institutions who have contributed  ... 
doi:10.1371/journal.pbio.1001046 pmid:21526222 pmcid:PMC3079585 fatcat:cfshtutffzhfvdqgwnda2sxlym

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

Peng He, Brian A. Williams, Diane Trout, Georgi K. Marinov, Henry Amrhein, Libera Berghella, Say-Tar Goh, Ingrid Plajzer-Frick, Veena Afzal, Len A. Pennacchio, Diane E. Dickel, Axel Visel (+4 others)
2020 Nature  
We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular  ...  The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif  ...  Sample size Two bioreplicates are the ENCODE standard sampling, supporting IDR for companion chromatin data. The bulk RNA-Seq libraries match the chromatin samples.  ... 
doi:10.1038/s41586-020-2536-x pmid:32728245 pmcid:PMC7410830 fatcat:luwwbtcvwjhmxkltuoraiq2fte

eXframe: reusable framework for storage, analysis and visualization of genomics experiments

Amit U Sinha, Emily Merrill, Scott A Armstrong, Tim W Clark, Sudeshna Das
2011 BMC Bioinformatics  
Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration  ...  Results: We have developed eXframe -a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple  ...  Acknowledgements We would like to acknowledge the Harvard Stem Cell Institute (HSCI) for funding and support. We thank Dr. Daniel Tenen, Dr. David Scadden, Dr. Len Zon, Dr. Stuart Orkin and Dr.  ... 
doi:10.1186/1471-2105-12-452 pmid:22103807 pmcid:PMC3235155 fatcat:w4xj72om4rcttnhrnxzbxkwyze

High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states

Siqi Tian, Pablo Cordero, Wipapat Kladwang, Rhiju Das
2014 RNA: A publication of the RNA Society  
Computational support estimates, data from alternative chemical probes, and mutate-and-map (M(2)) experiments highlight issues of prior methodology and instead give a near-crystallographic secondary structure  ...  These results correct an erroneous SHAPE inference of a ribosomal conformational change, expose critical limitations of conventional structure mapping methods, and illustrate practical steps for more incisively  ...  ACKNOWLEDGMENTS We acknowledge financial support from a Stanford Graduate Fellowship (S.T.), a Conacyt fellowship (P.C.), the Burroughs Wellcome Foundation (CASI to R.D.), and NIH R01 R01GM102519.  ... 
doi:10.1261/rna.044321.114 pmid:25183835 pmcid:PMC4201832 fatcat:xxbufh5ywjftbgdosb3l4lujky

The UCSC Genome Browser Database: 2008 update

D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller (+13 others)
2007 Nucleic Acids Research  
The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line  ...  This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for  ...  and sharing (40) .  ... 
doi:10.1093/nar/gkm966 pmid:18086701 pmcid:PMC2238835 fatcat:zdlffcr2vvhpdhn5epwzsneyky

OUP accepted manuscript

2016 Nucleic Acids Research  
The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line  ...  This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for  ...  and sharing (40) .  ... 
doi:10.1093/nar/gkw1134 pmid:27899642 pmcid:PMC5210591 fatcat:h6hqicfojzaifoxt3ndyhoy5pi

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

Daniel J Hogan, Daniel P Riordan, André P Gerber, Daniel Herschlag, Patrick O Brown, Sean R. Eddy
2008 PLoS Biology  
To test this hypothesis and to extend and deepen our understanding of RBP-RNA interactions, we systematically searched for the RNA targets of a select sample of 40 out of the more than 500 known and predicted  ...  Steps in RNA processing in the nucleus are functionally and physically coupled, providing an opportunity for coordinated control [23] .  ...  We thank Maitreya Dunham, Donna Storton, Joseph DeRisi, and Adam Carroll and members of the Brown and Herschlag labs for advice and discussions.  ... 
doi:10.1371/journal.pbio.0060255 pmid:18959479 pmcid:PMC2573929 fatcat:zwfe46biinbc5eoig5fxrlauli

The Immunological Genome Project: networks of gene expression in immune cells

Tracy S P Heng, Michio W Painter, Kutlu Elpek, Veronika Lukacs-Kornek, Nora Mauermann, Shannon J Turley, Daphne Koller, Francis S Kim, Amy J Wagers, Natasha Asinovski, Scott Davis, Marlys Fassett (+26 others)
2008 Nature Immunology  
ACKNOWLEDGMENTS We thank eBiosciences, Affymetrix and Expression Analysis for participation and support.  ...  Supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (R24 AI072073 to C.B.).  ...  ) RNA Cells 'Metadata' Graphic structures Computational biologists BU Stanford Scientific visualization Immunologists Raw data 'Clean' data Data analysis Biological curation  ... 
doi:10.1038/ni1008-1091 pmid:18800157 fatcat:hbupcrf43fb2pkckqovq5eugxi
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