Scout Report Selection, November 29, 1996
The Scout Report is the flagship publication of the Internet Scout Project. Published every Friday both on the web
and by email, it provides a fast, convenient way to stay informed of valuable resources on the Internet. The Internet Scout Project is located in the
Department of Computer Sciences at the University of Wisconsin-Madison, and is funded by a grant from the
National Science Foundation. The Scout Report description of the Interactive Fly states "...this site offers users the benefit of a great deal of original research into the genes involved in the development of the fruit fly."
News announcement June, 1997
Human Genome News (HGN) is a newsletter of the U.S. Human Genome Project sponsored by the genome
program of the Department of Energy Office of Biological and Environmental Research. HGN is intended to
facilitate communication among genome researchers and to inform persons interested in genome research. The announcement "FlyBase Updated" includes the fact that FlyBase servers "now provide access to the Interactive Fly...FlyBase has
developed a hierarchy of the Interactive Fly that links to specific pages, and gene lists link to individual gene records
in both FlyBase and the Interactive Fly." HGN, January-June 1997; 8:(3 & 4)
2 star rating from BioMedLink December 8, 1997
BioMedNet "The Worldwide Club for the
Biological and Medical Community," maintains BioMedLink, an evaluated and annotated data base of internet resources. Use of BioMedLink is free to viewers, but does require registration (user name and password). The BioMedLink evaluation of the Interactive Fly says "this is an excellent site for anyone interested in Drosophila and neurobiology."
Netwatch Site Visit
Science Magazine Vol. 280, May 15, 1998
Netwatch section: Delving Into Drosophila, edited by Jocelyn Kaiser. Available on-line by subscription.
Kaiser writes: "Loaded with information on protein function, mutation effects, homologous genes and other organisms, and links to Medline abstracts, the site is 'the only place where you can go up and down the hierarchy' of development, says Brody, adding, 'it explains what the [Human] Genome Project is about.'"
Flies Invade Human Genetics, by Ricki Lewis in The Scientist, Volume 12, No. 13, June 22, 1998.
The Scientist, "the newspaper for the life sciences professional," is issued bi-weekly, and is available free on-line and/or by mail subscription for a fee. The Lewis article presents parallels between gene function in Drosophila and humans, and explains why Drosophila is an ideal organism for studying the roles genes play in development. Beautiful photographic illustrations.
An HMS Beagle Webpick
Web Resources of Model Organisms, by Pamela M. Gannon, July 24, 1998 in issue 35 of HMS Beagle, the journal of BioMedNet. Gannon says: "The Interactive Fly...is an excellent, general informational resource for Drosophila designed to showcase Drosophila genes and their roles in development."
Mighty Fruit Fly, Atlas of DNA Research, by Judy Silber, in
The Christian Science Monitor, August 27, 1998. The article chronicles the history of Drosophila research and explains how Drosophila became the organism of choice for the study of biological processes. The article provides a link to The Interactive fly.
Site of the Day October 20, 1998
Selected by New Scientist Planet Science, the award winning online voice of New Scientist, a weekly magazine of science and technology. Site of the Day is a feature
in the Keysites section, which covers internet related
topics. Archived in Hotspots, the citation states: "...the Interactive Fly is a convenient and well-organised compendium of information...The extensive list of fly genes gives more information about the structure and function of each gene than do many printed references."
Internet Resource August 1999
An article about The Interactive Fly in Trends in Genetics describes the history and future of web based gene network resources:
Brody, T. (1999). The Interactive Fly: gene networks, development and the Internet. Trends in Genetics 15 (8): 333-4. 10431196
Academic Research on the Internet: Options for Scholars and Libraries Edited by Helen Laurence, William Miller, Haworth Press, 2000. This book allows you to "find what youre looking for with the best Internet resources for academic research in the humanities, sciences, and social sciences." John Sisson, in a chapter entitled "Biology Sites on the World Wide Web: a brief survey", writes about The Interactive Fly: "This is an excellent example of the kind of information that an individual can gather together as a resource and develop into a definitive source."
Sci/Tech Web Award June 2002
Scientific American has cited The Interactive Fly among its second annual Scientific American.com Sci/Tech Web Awards. In a section on Biology web resources the citation reads: "Find out about bazooka, eyeless, lame duck, shaggy and all the rest: this cyberspace guide to the myriad fruit fly (Drosophila) genes and their control functions is a monumental magnum opus that has become a standard in the field of developmental biology."
News Article September 2002
The NIH Catalyst is a bimonthly publication written for and by intramural scientists of the National Institutes of Health to foster communication and collaboration across NIH institutes. An article titled Brody's Site: No Fly-by-night, written by Rashmi Nemade, summarizes the history and content of the The Interactive Fly. The article describes the Interactive Fly website as a resource in which the "novice or expert can maneuver through and grasp the Drosophila genome with just a few clicks."
Sequence - Evolution - Function : Computational Approaches in Comparative Genomics by Eugene V. Koonin, Michael Y. Galperin, Kluwer Academic Publishing, 2002.
This book is 'an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics.' Koonin and Gilperin write, "The Interactive Fly is a superb collection of information on tissue and organ development in Drosophila." They continue, 'arguably, the most interesting part of the database is the listing of 36 evolutionarily conserved developmental pathways, common for Drosophila and other organisms, such as vertebrates.+
Netwatch Site Visit December 2004
Science, Vol. 306, Issue 5702, 1661. DATABASE: To Build a Fly.
"An inert egg can't morph into a flitting fruit fly without tinman and Mothers against dpp, klumpfuss and knirps, legless, heartless, tailless, and hairless. Find out how these and more than 600 other genes mold Drosophila development at the Interactive Fly, created 9 years ago by neurogeneticist Thomas Brody of the National Institute of Neurological Disorders and Stroke and hosted by the Society for Developmental Biology. The site also brims with background information on fly formation, including a developmental atlas."
STRING uses The Interactive Fly for text parcing January 2005
Nucleic Acid Research 33: D433-D437.
Christian von Mering and Lars J. Jensen, et al. (2005) of the
European Molecular Biology Laboratory in Heidelberg, Germany, developed STRING ('Search Tool for the Retrieval of Interacting Genes/Proteins') to simplify access to information by providing a comprehensive collection of protein-protein associations for a large number of organisms. The associations are derived from high-throughput experimental data, from the mining of databases and literature, and from predictions based on genomic context analysis. The associations are extended beyond the organism in which they were originally described, by automatic transfer to orthologous protein pairs in other organisms. STRING parses Medline, OMIM, and The Interactive Fly, and currently holds 730,000 proteins in 180 fully sequenced organisms.
FlyExpress, an express pattern search engine, provides links to The Interactive Fly. April 2006
Sudhir Kumar and Bernard Van Emden of Arizona State University, Tempe, along with a host of students and collaborators. have developed
FlyExpress, an image-matching search engine, for finding biologically similar gene expression patterns. Genes with overlapping expression patterns can be discovered using the Basic Expression Search Tool for images (BESTi). Expression patterns can be retrieved by entering gene names, synonyms, ontology terms and keywords. FlyExpress and The Interactive Fly maintain cross-links to one another to provide cross reference of images and text concerning Drosophila gene expression.
Citation November 2005
J. Insect Sci. 5: 3.
Effects of carbon dioxide narcosis on ovary activation and gene expression in worker honeybees, Apis mellifera by Preeyada Koywiwattrakul, Graham J Thompson, Sririporn Sitthipraneed, Benjamin P Oldroyd, and Ryszard Maleszka.
In an effort to uncover genes associated with ovary activation in honey bee workers, the extent to which eight candidate genes co-varied in their expression with experimentally-induced changes in worker reproductive state was examined. The results show that the expression of vitellogenin and transferrin is correlated with ovary activation in workers, and may therefore be part of the gene network involved in the regulatory control of functional sterility in honeybees. Selection of candidate genes for this study was based their functional gene descriptions at Interactive Fly.
Citation February, 2006
Biostatistics 7: 569-584.
Time ordering of gene coexpression by Xiaoyan Leng and Hans-Georg Müller.
Temporal microarray gene expression profiles allow characterization of gene function through time dynamics of gene coexpression within the same genetic pathway. This paper defined and estimated a global time shift characteristic for each gene via least squares, inferred from pairwise curve alignments. These time shift characteristics of individual genes reflect a time ordering that is derived from observed temporal gene expression profiles. Once these time shift characteristics are obtained for each gene, they can be entered into further analyses, such as clustering. The proposed methodology is illustated using Drosophila embryonic development and yeast cell-cycle gene expression profiles, as well as simulations. Feasibility is demonstrated through the successful recovery of time ordering. Estimated time shifts for Drosophila maternal and zygotic genes, curated from The Interactive Fly, provide excellent discrimination between these two categories and confirm known genetic pathways through the time order of gene expression.
Citation January, 2007
Mol Syst Biol. 3: 72.
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis by Sean D Hooper, Stephanie Boué, Roland Krause, Lars J. Jensen, Christopher E. Mason, Murad Ghanim, Kevin P. White, Eileen E. M. Furlong, and Peer Bork.
A time-series analysis of whole-genome expression data during Drosophila melanogaster development indicates that up to 86% of its genes change their relative transcript level during embryogenesis. By applying conservative filtering criteria and requiring 'sharp' transcript changes, 1534 maternal genes, 792 transient zygotic genes, and 1053 genes whose transcript levels increase during embryogenesis were recovered. Each of these three categories is dominated by groups of genes where all transcript levels increase and/or decrease at similar times, suggesting a common mode of regulation. Common and distinctive functional features of these expression groups, classified in part through the use of The Interactive Fly database, were highlighted and a coupling between downregulation of transcript levels and targeted protein degradation was demonstrated. By mapping the groups to the protein network, new functional associations were predicted and experimentally confirmed.
Listing of COPUS Network Participants
The Coalition on the Public Understanding of Science (COPUS)
highlights The Society for Developmental Biology and their resource, The Interactive Fly. COPUS is a grassroots effort linking universities, scientific societies, science centers and museums, advocacy groups, media, educators, businesses, and industry in a peer network having as its goal a greater public understanding of the nature of science and its value to society.
In their citation, COPUS states that The Society for Developmental Biology (SDB) was founded in 1939 to promote the field of developmental biology and to advance understanding of developmental biology at all levels. To this end, within developmental biology, the SDB fosters excellence in research and education, provide advice and resources on careers, and provides information for the public. Perhaps most importantly, the SDB provides a communication hub for all developmental biologists. About The Interactive Fly, the citation states that this resource "provides an immense body of information on the development of Drosophila melanogaster."
Citation September, 2008
Evolution & Development 10: 583590.
Microevolutionary support for a developmental hourglass: gene expression patterns shape sequence variation and divergence in Drosophila by Tami Cruickshank, and Michael J. Wade.
Sequence variation was analyzed of five gene classes, curated from The Interactive Fly, that act sequentially to shape early embryo development in Drosophila: maternal, gap, pair-rule, segment polarity, and segment identity genes. Two related patterns were found: (1) a microevolutionary pattern, wherein relative sequence variation within species is 2- to 3-fold higher for maternal-effect genes than for any other gene class; and, (2) a macroevolutionary pattern, wherein the relative sequence divergence among species for maternal-effect genes is 2- to 4-fold greater than for any other gene class. Both patterns are qualitatively and quantitatively consistent with the predictions of microevolutionary theory. These findings connect within-species genetic variation to between-species divergence and shed light on the controversy over the existence of a 'developmental hourglass,' where mid-embryonic stages are more evolutionarily constrained than either earlier or later stages.
Citation August 2010
PloS ONE 5: e12139
A Genome-Wide Gene Function Prediction Resource for
Drosophila melanogaster by Han Yan, Kavitha Venkatesan, John E. Beaver, Niels Klitgord, Muhammed A. Yildirim, Tong Hao, David E. Hill, Michael E. Cusick, Norbert Perrimon, Frederick P. Roth, Marc Vidal
Predicting gene functions by integrating large-scale biological data remains a challenge for systems biology. This paper
presents a resource for Drosophila melanogaster gene function predictions. Function-specific classifiers were trained to
optimize the influence of different biological datasets for each functional category. The model predicted GO terms and KEGG pathway memberships for Drosophila melanogaster genes with high accuracy, as affirmed by cross-validation,
supporting literature evidence, and large-scale RNAi screens. The resulting resource of prioritized associations between Drosophila genes and their potential functions offers a guide for experimental investigations. Three well-known pathways not yet represented in KEGG - JNK Signaling, Insulin/AKT and Hippo pathways - were included
based on information from The Interactive Fly Database
Citation July 2011
PloS ONE 6(7):e21504.
Comparative genomic analysis of Drosophila melanogaster and vector mosquito developmental genes. by Susanta K. Behura, Morgan Haugen, Ellen Flannery, Joseph Sarro, Charles R. Tessier, David W. Severson, Molly Duman-Scheel
Developmental genes of D. melanogaster were chosen based on Gene Ontology annotation in FlyBase (http://flybase.net), through information posted in Interactive Fly, through literature surveys, and in reference to the genes selected for a recently published comprehensive survey of developmental genes in A. pisum (https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2583.2009.00944.x). Orthology calls were prepared with the aid of several databases: Biomart (http://www.biomart.org/biomart/martview/), Vectorbase (http://www.vectorbase.org/), Flybase (http://flybase.org/), OrthoDB (http://cegg.unige.ch/orthodb4), InParanoid (http://inparanoid.cgb.ki.se/), and (miRBase http://www.mirbase.org/).
Citation June 2019
PloS ONE 6(7):e21504.
Identification of key modules and hub genes for small-cell lung carcinoma and large-cell neuroendocrine lung carcinoma by weighted gene co-expression network analysis of clinical tissue-proteomes by Haruhiko Nakamura, Kiyonaga Fujii, Vipul Gupta, Hiroko Hata, Hirotaka Koizumu , Masahiro Hoshikawa, Saeko Naruki, Yuka Miyata, Ikuya Takahashi, Tomoyuki Miyazawa, Hiroki Sakai, Kouhei Tsumoto, Masayuki Takagi, Hisashi Saji, Toshihide Nishimura
This study provides an understanding of the molecular differences in tumorigenesis and malignancy between SCLC and LCNEC and may help identify potential therapeutic targets. This study utilized STRING which integrates protein–protein interactions obtained from multiple databases (IntAct, Reactome, DIP (Database of Interacting Proteins)], BioGRID, MINT (The Molecular INTeraction Database), KEGG (the Kyoto Encyclopedia of Genes and Genomes), NCI/Nature PID (National Cancer Institute—Nature Pathway Interaction Database), The Interactive Fly, and BioCyc) and protein–protein interactions computationally predicted by several state of the art algorithms that use gene expression data, genomics context, orthology-based analyses, and automated text mining analyses.