Differences among hemoglobin thresholds for red blood cell transfusions in patients with hematological diseases in teaching hospitals: a real world data in Japan.

A hemoglobin (Hb) threshold level of 7 g/dL has been proposed for red blood cell (RBC) transfusion in patients with chronic anemia in the Japanese guideline since 2005. However, Hb thresholds for hematological diseases in clinical practice and factors responsible for higher Hb thresholds remain unclear. Hb thresholds were collected for patients with hematological diseases from 32 Japanese teaching hospitals.

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters.

The identification of orthologous genes in an increasing number of fully sequenced genomes is a challenging issue in recent genome science. Here we present KEGG OC (http://www.genome.

Virtual metagenome reconstruction from 16S rRNA gene sequences.

Microbial ecologists have investigated roles of species richness and diversity in a wide variety of ecosystems. Recently, metagenomics have been developed to measure functions in ecosystems, but this approach is cost-intensive. Here we describe a novel method for the rapid and efficient reconstruction of a virtual metagenome in environmental microbial communities without using large-scale genomic sequencing.

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

Background: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009.

CGAS: comparative genomic analysis server.

Summary: Comparative approach is one of the most essential methods for extracting functional and evolutionary information from genomic sequences. So far, a number of sequence comparison tools have been developed, and most are either for on-site use, requiring program installation but providing a wide variety of analyses, or for the online search of user's sequences against given databases on a server. We newly devised an Asynchronous JavaScript and XML (Ajax)-based system for comparative genomic analyses, CGAS, with highly interactive interface within a browser, requiring no software installation.

KEGG Atlas mapping for global analysis of metabolic pathways.

KEGG Atlas is a new graphical interface to the KEGG suite of databases, especially to the systems information in the PATHWAY and BRITE databases. It currently consists of a single global map and an associated viewer for metabolism, covering about 120 KEGG metabolic pathway maps and about 10 BRITE hierarchies. The viewer allows the user to navigate and zoom the global map under the Ajax technology.

Network analysis of adverse drug interactions.

Harmful effects associated with use of drugs are caused as a result of their side effects and combined use of different drugs. These drug interactions result in increased or decreased drug effects, or produce other new unwanted effects and are serious problems for medical institutions and pharmaceutical companies. In this study, we created a drug-drug interaction network from drug package inserts and characterized drug interactions.

KEGG for linking genomes to life and the environment.

KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information.

Evolutionary history and functional implications of protein domains and their combinations in eukaryotes.

Background: In higher multicellular eukaryotes, complex protein domain combinations contribute to various cellular functions such as regulation of intercellular or intracellular signaling and interactions. To elucidate the characteristics and evolutionary mechanisms that underlie such domain combinations, it is essential to examine the different types of domains and their combinations among different groups of eukaryotes.

Results: We observed a large number of group-specific domain combinations in animals, especially in vertebrates.

KAAS: an automatic genome annotation and pathway reconstruction server.

The number of complete and draft genomes is rapidly growing in recent years, and it has become increasingly important to automate the identification of functional properties and biological roles of genes in these genomes. In the KEGG database, genes in complete genomes are annotated with the KEGG orthology (KO) identifiers, or the K numbers, based on the best hit information using Smith-Waterman scores as well as by the manual curation. Each K number represents an ortholog group of genes, and it is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy.

Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes.

Recent evidence points to the existence of scale-free properties in many biological networks. By topological analysis, several models including preferential attachment and hierarchical modules have been proposed to explain how these networks are organized. On the other hand, analyses using dynamics have suggested that gene expression and metabolic networks have been organized with the scale-free property by the other models such as "rich-travel-more" and "log-normal dynamics.

Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic.

The SNARE proteins are required for membrane fusion during intracellular vesicular transport and for its specificity. Only the unique combination of SNARE proteins (cognates) can be bound and can lead to membrane fusion, although the characteristics of the possible specificity of the binding combinations encoded in the SNARE sequences have not yet been determined. We discovered by whole genome sequence analysis that sequence motifs (conserved sequences) in the SNARE motif domains for each protein group correspond to localization sites or transport pathways.

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.

Expressed sequence tag (EST) sequencing has proven to be an economically feasible alternative for gene discovery in species lacking a draft genome sequence. Ongoing large-scale EST sequencing projects feel the need for bioinformatics tools to facilitate uniform EST handling. This brings about a renewed importance for a universal tool for processing and functional annotation of large sets of ESTs.

From genomics to chemical genomics: new developments in KEGG.

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.

Clustering of database sequences for fast homology search using upper bounds on alignment score.

Homology data are among the most important information used to predict the functions of unknown proteins and thus fast and accurate methods are needed. In this paper, we propose a new approach for fast and accurate homology search using pre-computed all-against-all similarity scores in a target database. We previously developed a method for derivation of an upper bound of the Smith-Waterman score (SW-score) between a query and a homolog candidate sequence using the SW-score between the candidate and a sequence similar to the query.

Using protein motif combinations to update KEGG pathway maps and orthologue tables.

We have studied the projection of protein family data onto single bacterial translated genome as a solution to visualise relationships between families restricted to bacterial sequences. Any member of any type of family as defined in the Pfam database (domains, signatures, etc.) is considered as a protein module.

Fast and accurate database homology search using upper bounds of local alignment scores.

Motivation: It is widely recognized that homology search and ortholog clustering are very useful for analyzing biological sequences. However, recent growth of sequence database size makes homolog detection difficult, and rapid and accurate methods are required.

Results: We present a novel method for fast and accurate homology detection, assuming that the Smith-Waterman (SW) scores between all similar sequence pairs in a target database are computed and stored.

Extraction of organism groups from phylogenetic profiles using independent component analysis.

In recent years, the analysis of orthologous genes based on phylogenetic profiles has received popularity in bioinfomatics. We propose a new method to extract organism groups and their hierarchy from phylogenetic profiles using the independent component analysis (ICA). The method involves first finding independent axes in the projected space from the multivariate data matrix representing phylogenetic profiles for a number of orthologous genes.