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FlyTF

http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/

Description :
FlyTF is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified TFs from the literature. The data is available for case-by-case query (featuring a search form for various TF characteristics) and for bulk download.

Recent develoments :
We encourage the Drosophila community to provide feedback on our annotations. Future releases and updates to the database based on user feedback are planned, and the incorporation of the "12 Genomes" is underway. The FlyTF data is now available as "public bags" in FlyMine (http://www.flymine.org).

Aknowledgement :
Work on FlyTF was enabled through an EMBO Longterm Fellowship to BA, and SAT is an EMBO Young Investigator.

References :
1. Adryan, B. and Teichmann, S.A. (2006) FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics 22(12): 1532
2. Adryan, B. and Teichmann, S.A. (2007). Computational Identification of Site-Specific Transcription Factors in Drosophila. Fly 1(3): 142

MachiBase

http://machibase.gi.k.u-tokyo.ac.jp/

Description :
Drosophila melanogaster 5 mRNA transcription start site database

REDfly

http://redfly.ccr.buffalo.edu/

Description :
Regulatory modules and transcription factor binding sites in Drosophila

FlyEx

http://flyex.ams.sunysb.edu/flyex

Description :
FlyEx is a spatiotemporal atlas of segmentation gene expression. The important feature that sets FlyEx apart from other spatiotemporal atlases is the availability of highly accurate quantitative gene expression data. FlyEx supports operations on images of gene expression patterns and allows a user to monitor and analyze the dynamics of formation of segmentation gene expression domains over the whole period of segment determination, that amounts to 1.5 h of development.

Aknowledgement :
FlyEx development is supported by the National Institutes of Health (RR07801) and the Grant Assistant Program of the Civilian Research and Development Foundation (RUB1-1578-ST-05).

References :
1Poustelnikova, E., Pisarev, A., Blagov, M., Samsonova, M., and Reinitz, J. (2004). A database for management of gene expression data in situ. Bioinformatics, 20: 2212-2221.2Samsonova, M., Pisarev, A., and Blagov, M. (2003). Processing of natural language queries to a relational database. Bioinformatics, 19, Suppl. 1, i241-i249.

FLYSNP

http://flysnp.imp.univie.ac.at/

Description :
SNP data for Drosophila melanogaster

DroID - Drosophila Interactions Database

http://www.droidb.org/

Description :
DroID, the Drosophila Interactions Database, assembles gene and protein interaction data from a variety of sources into one easily accessible, comprehensive database. The database includes published and unpublished low and high throughput data sets, genetic interactions, and computationally predicted interactions. The predicted interactions are generated based on interactions found in other organisms. The database can be searched using gene and protein information available from Flybase. DroID also includes gene expression data that can be used to filter interaction data. DroID can be accessed through a standard web page or by using IM Browser, a program for exploring multiple data sets and for graphically mapping the interactions. Use of the IM Browser requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. All of the data in DroID can be freely downloaded in a variety of formats compatible with analysis tools. The database and IM Browser are accessible from http://www.droidb.org.

Recent develoments :
Data from other public databases has been incorporated and new computational predictions have been added. A semi-automated update regime has been instituted to ensure the latest data availability. A new web interface enables rapid searches with results linked to IM Browser for drawing interaction maps. New IM Browser features include filtering on gene expression data and the ability to load a local set of interactions. A new Cytoscape plug-in is also available for accessing DroID.

Aknowledgement :
This work was supported by NIH grant HG001536, and the National Center for Proteome and Pathway Mapping, NIH grant P41 RR18327.

References :
1. Pacifico S, Liu G, Guest S, Parrish JR, Fotouhi F, Finley RL Jr. (2006) A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. BMC Bioinformatics 7:195.

UCSC Fruitfly Genome Browser Gateway

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

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

Berkeley Drosophila Genome Project

http://www.fruitfly.org/

Description :
Good entrez to fly genome resources.

Ensembl Drosophila Genome Browser

http://www.ensembl.org/Drosophila_melanogaster/

Description :
Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).

FlyBase

http://flybase.bio.indiana.edu/

Description :
FlyBase is a database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae; the primary species represented is Drosophila melanogaster.

Genome Biology Release 3 of the Drosophila genome

http://genomebiology.com/drosophila/

Description :
A series of refereed research articles describing Release 3 of the Drosophila genome are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies.

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.

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