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UTRome

http://www.utrome.org/

Description :
3 UTRs and their functional elements in C. elegans

CMGSDB

https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/

Description :
Computational models for gene silencing in C. elegans

UCSC C. elegans Genome Browser Gateway

http://genome.ucsc.edu/cgi-bin/hgGateway?org=C.+elegans&db=0&hgsid=27736277

Description :
Provides a rapid and reliable display of any requested portion of the C. elegans genome at any scale, together with dozens of aligned annotation tracks.

UCSC C. briggsae Genome Browser Gateway

http://genome.ucsc.edu/cgi-bin/hgGateway?org=C.+briggsae&db=0&hgsid=27736277

Description :
Provides a rapid and reliable display of any requested portion of the C. briggsae genome at any scale, together with dozens of aligned annotation tracks.

Ensembl C.elegans Genome Browser

http://www.ensembl.org/Caenorhabditis_elegans/

Description :
Access the data through the Ensembl user interface (both for visualisation and data mining) to provide cross-species integration throughout Ensembl s comparative genomics resources.

WormBase

http://www.wormbase.org/

Description :
Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.

C. elegans Gene Knockout Consortium

http://www.celeganskoconsortium.omrf.org/

Description :
Worldwide consortium whose ultimate goal is to produce null alleles of all known genes in the C. elegans genome; submit your gene to the knockout list.

Interolog/Regulog Database

http://interolog.gersteinlab.org/

Description :
Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.

BioGRID

http://www.thebiogrid.org/

Description :
Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at http://www.thebiogrid.org. BioGRID release version 2.0 includes more than 116,000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.

Recent develoments :
Over 30,000 protein and genetic interactions have recently been added from 5,778 sources through exhaustive curation of the S. cerevisiae primary literature (Reguly et al, submitted). An analogous systematically curated set of interactions compiled from the Schizosaccharomyces pombe (fission yeast) literature will also be deposited shortly. Selected physical interaction datasets for TGF-b, TOR and cancer networks in mammalian cells will also be deposited in the near future. A new quantitative genetic interaction experimental descriptor has been added to accommodate recent Epistatic Mini-Array Profiles (E-MAP) and other forms of quantitative genetic interaction data generated in S. cerevisiae.

Gene Aging Nexus

http://gan.usc.edu/

Description :
Gene Aging Nexus (GAN, http://gan.usc.edu) is a data mining platform for the biogerontological-geriatric research community. It enables users to analyze, query, and visualize the aging-related genomic data. Our goal is to facilitate the digestion and usage of the public genomic data. A current focus is on integrative analysis of microarray gene expression data. We are establishing a central database for aging microarray data of six species: human (H. sapiens), rat (R. norvegicus), mouse (M. musculus), fruit fly (D. melanogaster), worm (C. elegans), and yeast (S. cerevisiae). GAN is equipped with a set of bioinformatics tools for analysis of the microarray data sets, cross-platform and cross-species.

Aknowledgement :
The work was supported by a pilot grant from the Seaver foundation, the NIH Grants R01GM074163, P50HG002790, P01AG14751, R01AG13499, and the NSF grant 0515936

CellCircuits

http://www.cellcircuits.org/

Description :
CellCircuits (http://www.cellcircuits.org) is an open-access database of molecular network models, designed to bridge the gap between databases of individual pair-wise molecular interactions and databases of validated pathways. CellCircuits captures the output from an increasing number of approaches that screen molecular interaction networks to identify functional subnetworks, based on their correspondence with expression or phenotypic data, their internal structure, or their conservation across species. This initial release catalogs 2019 computationally-derived models drawn from eleven journal articles and spanning five organisms (yeast, worm, fly, Plasmodium falciparum, and human). Models are available either as images or in machine-readable formats and can be queried by the names of proteins they contain or by their enriched biological functions. We envision CellCircuits as a clearinghouse in which theorists may distribute or revise models in need of validation and experimentalists may search for models or specific hypotheses relevant to their interests. We demonstrate how such a repository of network models is a novel systems biology resource by performing several meta-analyses not currently possible with existing databases.

Aknowledgement :
We acknowledge funding from the National Science Foundation (NSF 0425926) and thank the members of the Ideker lab for testing and suggesting improvements to the web interface.

POINT

http://point.bioinformatics.tw/

Description :
One possible path towards understanding the biological function of a target protein is through the discovery of how it interfaces within protein-protein interaction networks. The goal of this study was to create a virtual protein-protein interaction model using the concepts of orthologous conservation (or interologs) to elucidate the interacting networks of a particular target protein. POINT (the prediction of interactome database) is a functional database for the prediction of the human protein-protein interactome based on available orthologous interactome datasets. POINT integrates several publicly accessible databases, with emphasis placed on the extraction of a large quantity of mouse, fruit fly, worm and yeast protein-protein interactions datasets from the Database of Interacting Proteins (DIP), followed by conversion of them into a predicted human interactome. In addition, protein-protein interactions require both temporal synchronicity and precise spatial proximity. POINT therefore also incorporates correlated mRNA expression clusters obtained from cell cycle microarray databases and subcellular localization from Gene Ontology to further pinpoint the likelihood of biological relevance of each predicted interacting sets of protein partners.

Aknowledgement :
We would like to thank DIP, GO, NCBI, PIR-NREF, UniProt for their public accessible databases and software that provided the foundation for construction of this applied POINT database. Development of the POINT database was supported by grants from the National Science Council (NSC92-3112-B-400-005) and National Health Research Institutes to C. F. H

Intronerator

http://hgwdev-hiram.cse.ucsc.edu/IntronWS120/

Description :
The Intronerator (http://hgwdev-hiram.cse.ucsc.edu/IntronWS120/) is a set of web-based tools for exploring RNA splicing and gene structure in C. elegans. It includes a display of predicted genes, cDNA alignments with the genomic sequence, a catalog of alternatively spliced genes, a database of introns and alignment data for C. briggsae sequences with the C. elegans genome. The cDNA alignments include over 100,000 ESTs and almost 1000 full length cDNAs. ESTs from embryos and mixed stage animals as well as full-length cDNAs can be compared in the alignment display with each other and with predicted genes. The alt-splicing catalog includes 844 open reading frames for which there is evidence of alternative splicing of pre-mRNA. The intron database includes 28478 introns, and can be searched for patterns near the splice junctions. Eight million bases of C. briggsae genomic sequence have been aligned with the C. elegans genome using the WABA algorithm (W.J. Kent and A.M. Zahler. 2000. Genome Res. 10:1115-1125), and this alignment data is accessible via the Tracks Display of Intronerator.

WormBook

http://www.wormbook.org/

Description :
WormBook (http://www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of C. elegans and related nematodes. It contains over 100 chapters, covering nearly every aspect of C. elegans research, from cell biology and neurobiology to evolution and ecology. WormBook also contains WormMethods, a collection of methods and protocols used by nematode researchers. WormBook also serves as the text companion to WormBase, the C. elegans model organism database. Objects such as genes, proteins, and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters contain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available.

Recent develoments :
WormBook content continues to expand, with new chapters and sections broadening and elaborating on its scope. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters. In addition to new topics, WormBook has also recently added several new features including Endnote compatibility and the option to download a zip file containing the entire contents of WormBook.

Aknowledgement :
We thank the members of WormBase for helpful discussions and assistance. Funding for WormBook has been provided by the NIH (P41 HG02223), The Genetics Society, Society for Developmental Biology, as well as the generous support of the editors of C. elegans II.

References :
1. Girard, L, Fiedler, T., Harris, T., Carvalho, F., Antoshechkin, I., Han, M., Sternberg, P., Stein, L., Chalfie, M. (2007) WormBook: the online review of C. elegans biology. Nucleic Acids Res. 35: in press.

ACeDB

http://www.acedb.org/

Description :
C. elegans, S. pombe, and human sequences and genomic information

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