Tables S3-S6 show the top 20 predicted putative interactions with our method. Interactions that appear in the ChEMBL database are marked with “[C]”, interactions in Drugbank are marked with “[D]”, and interactions in Kegg are marked with “[K]”. Interactions that appear in any of these databases are marked in bold. Detailed information about predicted putative interactions and those confirmed by...

The KEGG Orthology (KO) database was tested as a source for automated annotation of expressed sequence tags (ESTs). We used a control experiment where every EST was assigned to its cognate protein, and an annotation experiment where the ESTs were annotated by proteins from other organisms. Analyzing the results, we could assign classes to the annotation: correct, changed and speculated. The cor...

The LIPID MAPS Proteome Database (LMPD) is an object-relational database of lipid-associated protein sequences and annotations. The initial release contains 2959 records, representing human and mouse proteins involved in lipid metabolism. UniProt IDs were obtained based on keyword search of KEGG and GO databases, and this LMPD protein list was then enhanced with annotations from UniProt, Entrez...

We report on a new type of systematic annotation error in genome and pathway databases that results from the misinterpretation of partial Enzyme Commission (EC) numbers such as '1.1.1.-'. This error results in the assignment of genes annotated with a partial EC number to many or all biochemical reactions that are annotated with the same partial EC number. That inference is faulty because of the...

The KEGG (Kyoto Encyclopedia of Genes and Genomes) is a web-based system, where it is possible to view the metabolic pathways of organisms whose genomes have been completely sequenced. The metabolic pathways are presented as map diagrams where different reaction chains appear as chains and networks of substrates and enzymes. Each organism in KEGG has a set of metabolic maps where the correspond...

COFECO is a web-based tool for a composite annotation of protein complexes, KEGG pathways and Gene Ontology (GO) terms within a class of genes and their orthologs under study. Widely used functional enrichment tools using GO and KEGG pathways create large list of annotations that make it difficult to derive consolidated information and often include over-generalized terms. The interrelationship...

MOTIVATION Functional characterization of genes is of great importance for the understanding of complex cellular processes. Valuable information for this purpose can be obtained from pathway databases, like KEGG. However, only a small fraction of genes is annotated with pathway information up to now. In contrast, information on contained protein domains can be obtained for a significantly highe...

Biopathway databases have been developed, such as KEGG and EcoCyc, that compile interaction structures of biopathways together with biological annotations. However, these biopathways are not directly editable and simulatable. Thus, we have made an application, the Biopathway Executer (BPE), that reconstructs these two major biopathway databases to XML formats of modeling and simulation platform...