CSB Assignment Week 10

Assignments for Week 10

Note! This assignment is currently active. All significant changes will be announced on the mailing list.

 
 

Protein-protein interaction data is not trivial to work with. A large number of different databases each have their own standards, processes, focus, and the resulting data – while all nominally relating to the same genes – can be very hard to consolidate. iRefIndex is a database that endeavours to consolidate the different data sources, and iRefWeb makes the results available through a Web interface. In this assignment, read about the principles that went into constructing iRefWeb, this is informative regarding the issues and difficulties encountered. Then work through the exercises published recently by the iRefWeb authors.

Note that the iRefIndex is one of the databases provided through Cytoscape's File → Import → Network → Public Databases ... menu.

Pre-reading

Read about the iRefWeb ...

Turner et al. (2010) iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford) 2010:baq023. (pmid: 20940177)

[ PubMed ] [ DOI ] Abstract We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein-protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/

... and a follow up on how it adresses common curation problems

Turinsky et al. (2011) Interaction databases on the same page. Nat Biotechnol 29:391-3. (pmid: 21552234)

[ PubMed ] [ DOI ]

Exercises

Work through the exercises described in the following paper

Turinsky et al. (2014) Navigating the global protein-protein interaction landscape using iRefWeb. Methods Mol Biol 1091:315-31. (pmid: 24203342)

[ PubMed ] [ DOI ] Abstract iRefWeb is a bioinformatics resource that offers access to a large collection of data on protein-protein interactions in over a thousand organisms. This collection is consolidated from 14 major public databases that curate the scientific literature. The collection is enhanced with a range of versatile data filters and search options that categorize various types of protein-protein interactions and protein complexes. Users of iRefWeb are able to retrieve all curated interactions for a given organism or those involving a given protein (or a list of proteins), narrow down their search results based on different supporting evidence, and assess the reliability of these interactions using various criteria. They may also examine all data and annotations related to any publication that described the interaction-detection experiments. iRefWeb is freely available to the research community worldwide at http://wodaklab.org/iRefWeb .