Experimentally tested mammalian siRNAs
IDT SciTools is a suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures.
pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.
AsiDesigner is a design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs.
OligoWalk is an online sever for designing efficient siRNA targeting a given mRNA sequence. By calculating thermodynamic features of sense-antisense hybidization, OligoWalk predicts the free energy changes of oligonucleotides binding to a target RNA.
PhenomicDB is a multi-species genotype/phenotype database,integrating public genotype/phenotype data from a wide range of modelorganisms and Homo sapiens. Genotype and phenotype descriptions areobtained from Entrez Gene, OMIM, wormbase, flybase, and many othercollections. Phenotypes cover e.g. mutant screens, k.o. mice, or RNAinterference. In addition, clinical descriptions and naturally occurringmutants are also available. As phenotypes are linked to genes whichthemselves are grouped according to orthology, users can easily comparephenotypes of a gene of interest over a wide range of organisms. Likewise,users can discover genes involved in phenotypes as diverse as neural tubedefects, Alzheimer disease, apoptosis, or polyploidy.
Recent develoments :
In a recent effort, PhenomicDB has been redesigned and updatedto its current version 2.1, now offering also cellular phenotypes fromwhole-genome RNAi screens with detailed information on experimental design,ontology terms from the MGI s Mammalian Phenotype Ontology and keywords forcell lines and experimental assays. Also, direct linking from externalsources by search term or identifier is now possible.
1. Groth P, Pavlova N, Kalev I, Tonov S, Georgiev G, Pohlenz HDand Weiss B. (2007) PhenomicDB: A new cross-species Genotype/PhenotypeResource. Nuecleic Acids Res. 35 (Database issue): in press.
2. Groth Pand Weiss B. (2006) Phenotype data: a neglected resource in biomedicalresearch? Current Bioinformatics. 1: 347-358.
3. Kahraman A, Avramov A,Nashev LG, Popov D, Ternes R, Pohlenz HD and Weiss B. (2005) PhenomicDB: amulti-species genotype/phenotype database for comparative phenomics.Bioinformatics. 21: 418-420.
Small RNAs (smRNAs), which include microRNAs (miRNAs), small-interfering RNAS (siRNAs) and trans-acting siRNAs (ta-siRNAs) are ~19-24 nt RNAs that are important negative regulators of nucleotide sequences involved in development, homeostasis and in the maintenance of heterochromatic states. The Cereals Small RNA Database (CSRDB) is an integrated resource for small RNAs expressed in rice and maize that includes a genome browser and a smRNA-target relational database as well as relevant bioinformatic tools. The resource currently contains a preliminary dataset of 35,454 and 68,871 mapped smRNA sequence reads for rice and maize respectively. Future updates will include smRNA data derived from different tissues and conditions. The database is accessible online at http://sundarlab.ucdavis.edu/smrnas/.
RNA interference (RNAi) has become a powerful tool for genetic screening in Drosophila. At the Drosophila RNAi Screening Center (DRSC), we are using a library of over 21,000 dsRNAs targeting known and predicted genes in Drosophila. This library is available for the use of visiting scientists wishing to perform full-genome RNAi screens. The data generated from these screens is collected in the DRSC database (http://flyRNAi.org/cgi-bin/RNAi_screens.pl) in a flexible format for the convenience of the scientist and for archiving data. The long-term goal of this database is to provide annotations for as many of the uncharacterized genes in Drosophila as possible. Data from published screens are available to the public through a highly configurable interface that allows detailed examination of the data and provides access to a number of other databases and bioinformatics tools.
Screening at the DRSC Visiting scientists typically perform their screens in duplicate - screening against two full-genome sets. Raw data from duplicate genome sets are collected along with phenotype and "hit" information. The scientists have password-protected accounts which give them access to data entry interfaces and direct links to their personal data, both published and unpublished. The logged in user also has access to some tools for viewing data a plate at a time, direct links to the bioinformatic tools (listed below), and functions for directly querying the quality control (QC) information for the source plates.
Website Overview The public database begins with a page listing all published screens that have been done at the DRSC. From there, the experimental data for each assay may be viewed in a configurable table. Where possible, links to the published papers and supplementary data are also provided. Also on the starting page are links to various informatic tools, a gene lookup function which provides extensive amplicon data, and a list of completed, but not yet published, screens.
The authors would like to thank Carolyn Shamu and Tim Mitchison of The Institute of Chemistry and Cell Biology (ICCB) at Harvard Medical School and Erik Brauner of the Broad Institute for all their help and guidance in setting up the early phase of the DRSC database. We would also like to thank Sara Cherry, Ramanuj Dasgupta, Kent Nybakken, Adam Friedman, Jennifer Philips and the rest of the Perrimon lab for their helpful suggestions on the web interface and feedback on the features of the database. This work was supported by grant R01 GM067761 from the National Institute of the General Medical Sciences. NP is a Howard Hughes Medical Institute investigator.
1. Armknecht, S., Boutros, M., Kiger, A., Nybakken, K., Mathey-Prevot, B. and Perrimon, N. (2005) High-throughput RNA interference screens in Drosophila tissue culture cells. Methods Enzymol, 392, 55-73.
2. Clemens, J.C., Worby, C.A., Simonson-Leff, N., Muda, M., Maehama, T., Hemmings, B.A. and Dixon, J.E. (2000) Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc Natl Acad Sci U S A, 97, 6499-6503.
3. Meister, G. and Tuschl, T. (2004) Mechanisms of gene silencing by double-stranded RNA. Nature, 431, 343-349.
4. Hild, M., Beckmann, B., Haas, S.A., Koch, B., Solovyev, V., Busold, C., Fellenberg, K., Boutros, M., Vingron, M., Sauer, F. et al. (2003) An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol, 5, R3. Epub 2003.
5. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F. et al. (2000) The genome sequence of Drosophila melanogaster. Science, 287, 2185-2195.
6. Agaisse, H., Burrack, L.S., Philips, J., Rubin, E.J., Perrimon, N. and Higgins, D.E. (2005) Genome-wide RNAi screen for host factors required for intracellular bacterial infection. Science, 14, 14.
7. Baeg, G.H., Zhou, R. and Perrimon, N. (2005) Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila. Genes Dev, 29, 29.
8. Boutros, M., Kiger, A.A., Armknecht, S., Kerr, K., Hild, M., Koch, B., Haas, S.A., Consortium, H.F., Paro, R. and Perrimon, N. (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science, 303, 832-835.
9. Cherry, S., Doukas, T., Armknecht, S., Whelan, S., Wang, H., Sarnow, P. and Perrimon, N. (2005) Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition. Genes Dev, 19, 445-452.
10. DasGupta, R., Kaykas, A., Moon, R.T. and Perrimon, N. (2005) Functional genomic analysis of the Wnt-wingless signaling pathway. Science, 308, 826-833.
11. Eggert, U.S., Kiger, A.A., Richter, C., Perlman, Z.E., Perrimon, N., Mitchison, T.J. and Field, C.M. (2004) Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol, 2, e379. Epub 2004 Oct 2005.
12. Kiger, A., Baum, B., Jones, S., Jones, M., Coulson, A., Echeverri, C. and Perrimon, N. (2003) A functional genomic analysis of cell morphology using RNA interference. J Biol, 2, 27. Epub 2003 Oct 2001.
13. Philips, J.A., Rubin, E.J. and Perrimon, N. (2005) Drosophila RNAi screen reveals CD36 family member required for mycobacterial infection. Science, 14, 14.
14. Qiu, S., Adema, C.M. and Lane, T. (2005) A computational study of off-target effects of RNA interference. Nucleic Acids Res, 33, 1834-1847. Print 2005.
15. Naito, Y., Yamada, T., Matsumiya, T., Ui-Tei, K., Saigo, K. and Morishita, S. (2005) dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. Nucleic Acids Res, 33, W589-591.
16. Gunsalus, K.C., Yueh, W.C., MacMenamin, P. and Piano, F. (2004) RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res, 32 Database issue, D406-410.
17. Arziman, Z., Horn, T. and Boutros, M. (2005) E-RNAi: a web application to design optimized RNAi constructs. Nucleic Acids Res, 33, W582-588.
Human siRNA database
Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense partners. They regulate sense genes at multiple levels and are implicated in various diseases. Using an improved whole-genome computational pipeline, we identified abundant cis-encoded exon-overlapping sense-antisense (SA) gene pairs in human, mouse, fly, and eight other eukaryotic species. We developed NATsDB (Natural Antisense Transcripts DataBase, http://natsdb.cbi.pku.edu.cn/) to enable efficient browsing, searching and downloading of this currently most comprehensive collection of SA genes, grouped into six classes based on their overlapping patterns. NATsDB also includes Non-exon-Overlapping Bidirectional (NOB) genes and Non-BiDirectional (NBD) genes. To facilitate the study of functions, regulations, and possible pathological implications, NATsDB includes extensive information about gene structures, polyA signals and tails, phastCons conservation, homologues in other species, repeat elements, EST expression profiles, and OMIM disease association.
NATsDB supports interactive graphical display of the alignment of all supporting EST and mRNA transcripts of the SA and NOB genes to the genomic loci. It supports advanced search by species, gene name, sequence accession number, chromosome location, coding potential, OMIM association, and sequence similarity.
Recent develoments :
Alternative isoforms identified with our SVAP (Splice Variant Analysis Platform) are presented as a new track, which is hoped to assist to investigate the potential association between antisense transcription and alternative splicing.
This work was supported by China Ministry of Science and Technology High Tech 863 Programs and China Ministry of Education "Program for New Century Excellent Talents in University". We thank the two anonymous reviewers for insightful suggestions. We thank Drs. Shunong Bai and Zicai Liang for helpful discussions, Dr. Osamu Ogasawara of DDBJ for support of BodyMap-Xs, and Shuqi Zhao and Ying Sun of Center for Bioinformatics for maintenance of computing resources.
1. Zhang, Y., Li, J., Kong L., Gao, G., Liu QR., and Wei L. (2007) NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res. 35, in press
RNAi Codex consists of a database of shRNA related information and an associated website. It has been developed as a portal for publicly available short-hairpin RNA (shRNA) resources and is accessible at http://codex.cshl.org. RNAi Codex currently holds data from the Hannon-Elledge shRNA library and allows the use of biologist-friendly gene names to access information on shRNA constructs that can silence the gene of interest. It is designed to hold user-contributed annotations and publications for each construct, as and when such data become available. RNAi Codex relies upon GeneSeer (http://geneseer.cshl.org) to handle gene names and has a variety of mapping information on genes, coding sequences and the location of the target sequences on the mRNA.
The siRNA database provides a gene-centric view of human siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by siSearch. Linked to these sequences is information including siRNA thermodynamic properties and the potential for sequence specific off-target effects. The database provides the user with sufficient data to evaluate the siRNAs potential inhibition and sequence-specific off target effects.
In release 1.0 there are 405 experimentally verified siRNAs targeting 50 genes, an average of 8 siRNAs/gene. It contains records and siRNA predictions for all genes in the REFSEQ curated human sequence set (20,410 "NM" sequences and 6767 "XM" sequences). The database is available at http://sirna.cgb.ki.se.
This work was supported by a grant from Pfizer Inc.
Antisense oligonucleotides (ODNs) technology is one of the important approaches for the sequence-specific knockdown of gene expression. ODNs have been used as research tools in the post-genome era, as well as new types of therapeutic agents. Since finding effective target sites within RNA is a hard work for antisense ODNs design, various experimental methods and computational approaches have been proposed. For better sharing the experimented and published ODNs, valid and invalid ODNs reported in literatures are screened, collected and stored in AOBase. Up to present, nearly 700 ODNs against 46 target mRNAs are contained in AOBase. Entries can be explored via TargetSearch and AOSearch web retrieval interfaces. AOBase can not only be useful in ODNs selection for gene function exploration, but also contribute to rules mining and algorithms developing for rational ODNs design.
GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by gene identifiers, RNAi probe identifiers as well as with Drosophila nucleotide or protein sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries.
Funding is provided by the Human Frontiers Science Program, the European Commission and the Deutsche Forschungsgemeinschaft
1. Horn T., Arziman Z., Berger J., Boutros M. (2007). GenomeRNAi: A Database for cell-based RNAi Phenotypes. Nucleic Acids Res. 35: in press