Title | ||
---|---|---|
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. |
Abstract | ||
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Background Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks
are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number
of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive
databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis.
One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins
or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of
interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to
many existing and emerging data sets.
Description Here we describe a comprehensive database ofDrosophilagene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions,
and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data
from different sources. The program, referred to as the Interaction Map (IM) Browser, is a web-based application for searching
and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and
minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed
to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated
with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined
searches and analyses based on either common or technique-specific attributes. The data can be visualized as an editable graph
and all or part of the data can be downloaded for further analysis with other tools for specific applications.The database
is available athttp://proteome.wayne.edu/PIMdb.html
Conclusion TheDrosophilaInteractions Database described here places a variety of disparate data into one easily accessible location. The database
has a simple structure that maintains all relevant information about how each interaction was determined. The IM Browser provides
easy, complete access to this database and could readily be used to publish other sets of interaction data. By providing access
to all of the available information from a variety of data types, the program will also facilitate advanced computational
analyses. |
Year | DOI | Venue |
---|---|---|
2006 | 10.1186/1471-2105-7-195 | BMC Bioinformatics |
Keywords | Field | DocType |
genetics,relational database system,web based applications,algorithms,database management systems,data type,microarrays,gene expression profiling,high throughput screening,systems integration,bioinformatics,biological process,internet,data integrity | Data integration,Data science,Graph,Data set,Computer science,Software,Relational database management system,Bioinformatics,Database,DNA microarray,System integration,The Internet | Journal |
Volume | Issue | ISSN |
7 | 1 | 1471-2105 |
Citations | PageRank | References |
27 | 0.59 | 13 |
Authors | ||
6 |
Name | Order | Citations | PageRank |
---|---|---|---|
Svetlana Pacifico | 1 | 50 | 1.84 |
Guozhen Liu | 2 | 31 | 1.04 |
Stephen Guest | 3 | 56 | 3.02 |
Jodi R Parrish | 4 | 28 | 1.06 |
Farshad Fotouhi | 5 | 1023 | 122.73 |
Russell L. Finley Jr. | 6 | 57 | 3.06 |