Ian Donaldson

iRefWeb is a resource that provides web interface to a large collection of protein–protein interactions aggregated from major primary databases. The underlying data-consolidation process, called iRefIndex, implements a rigorous methodology of identifying redundant protein sequences and integrating disparate data records that reference the same pept...

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...

Background Multigenic diseases are often associated with protein complexes or interactions involved in the same pathway. We wanted to estimate to what extent this is true given a consolidated protein interaction data set. The study stresses data integration and data representation issues. Results We constructed 497 multigenic disease groups from O...

Significance of overlaps between disease groups and binary data was calculated as described in the text. Number of interaction edges for each disease group is listed. Only those disease group overlaps with raw p-values less than 0.0004 are considered statistically significant.

Mapping of OMIM titles to disease groups and Entrez Gene identifiers.

The file can be opened in Cytoscape ( http://cytoscape.org ) to reproduce Figure 3 and explore disease groups and their overlaps with n-ary data in iRefIndex.

Overlaps between disease groups and regenerated complex data showing best overlaps and number of overlaps (complex span) before and after correction for multiple hypothesis testing. Example regenerated complexes have regular names that can be used to retrieve the binary interactions that make up the regenerated complex. For example: in the name “MI...

The file can be opened in Cytoscape ( http://cytoscape.org ) to reproduce Figure 1 and explore disease groups and their overlaps.

Overlaps between disease groups and n-ary records showing best overlaps (icrigid) and number of overlaps (complex span) before and after correction for multiple hypothesis testing. Additional information on n-ary records with the best overlap with a disease group can be found at http://wodaklab.org/iRefWeb/interaction/show/xxx where xxx is the icri...

Summary of disease groups in terms of both genes and proteins.

Background Previous studies have noted that drug targets appear to be associated with higher-degree or higher-centrality proteins in interaction networks. These studies explicitly or tacitly make choices of different source databases, data integration strategies, representation of proteins and complexes, and data reliability assumptions. Here we ex...

Supplementary Tables 1–6.

S2_R_Code_for_paper.txt. R script showing code to generate data and figures for this paper.

This is a plain text file that contains R code to reproduce all R analyses in the paper. See http://www.r-project.org/.

The iRefIndex addresses the need to consolidate protein interaction data into a single uniform data resource. iRefR provides the user with access to this data source from an R environment. The iRefR package includes tools for selecting specific subsets of interest from the iRefIndex by criteria such as organism, source database, experimental method...

The iRefIndex consolidates protein interaction data from ten databases in a rigorous manner using sequence-based hash keys. Working with consolidated interaction data comes with distinct challenges: data are redundant, overlapping, highly interconnected and may be collected and represented using different curation practices. These phenomena were qu...

The microtubule (MT) cytoskeleton is essential for a variety of cellular processes. MTs are finely regulated by distinct classes of MT-associated proteins (MAPs), which themselves bind to and are regulated by a large number of additional proteins. We have carried out proteome analyses of tubulin-rich and tubulin-depleted MAPs and their interacting...

To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood. A plethora of resources now exist to capture molecular interaction data from the many laboratories generating…

Genes that are upregulated in tumoricidal macrophages.

Bioinformatic analysis of genes upregulated in tumoricidal macrophages

Supplementary Figures S1-S9 and Supplementary Tables S1-S2

Genes that are downregulated in tumoricidal macrophages

The immune system can both promote and suppress cancer. Chronic inflammation and proinflammatory cytokines such as interleukin (IL)-1 and IL-6 are considered to be tumour promoting. In contrast, the exact nature of protective antitumour immunity remains obscure. Here, we quantify locally secreted cytokines during primary immune responses against my...

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 o...

Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact o...

Interaction data for a given protein may be spread across multiple databases. We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping. We present a method to generate a key for a protein interaction record...

Base excision repair (BER) is a major mode of repair of DNA base damage. BER is required for maintenance of genetic stability, which is important in the prevention of cancer. However, direct genetic associations between BER deficiency and human cancer have been difficult to firmly establish, and the first-generation mouse models deficient in indivi...

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researc...

The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the fo...

The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gen...

The Biomolecular Interaction Network Database (BIND; http://binddb.org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND 2.0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed...

Software to automate the process of extracting molecular interactions from three-dimensional (3D) structures has been developed that records these as Biomolecular Interaction Network Database (BIND) pairwise interaction records. Full annotation of BIND records is provided through a database processing tool called MMDBind, including detailed atom-at...

Text categorization tools make errors. However, if a justification is provided to explain why a document is assigned to a class, a user can sometimes verify the categorization without reading the entire document. In our work, the text categorization system processes abstracts from biomedical literature and distinguishes between those that report pr...

Atomic absorption spectroscopy demonstrated that highly purified RNA polymerase II from the yeast Saccharomyces cerevisiae binds seven zinc ions. This number agrees with the number of potential zinc-binding sites among the 12 different subunits of the enzyme and with our observation that the ninth largest subunit alone is able to bind two zinc ions...

Proteomics represents a collection of experimental approaches that may be used to investigate biological systems. Such approaches commonly produce vast amounts of data that relate to physical interactions between biomolecules. One challenge in extracting useful information from these data is determining how they relate to current knowledge. The goa...