Kyoto Encyclopedia Of Genes And Genomes Database Research Articles

Transcriptome profiling of pyrethroid resistant and susceptible mosquitoes in the malaria vector, Anopheles sinensis.

BackgroundAnopheles sinensis is a major malaria vector in China and other Southeast Asian countries, and it is becoming increasingly resistant to the insecticides used for agriculture, net impregnation, and indoor residual spray. Very limited genomic information on this species is available, which has hindered the development of new tools for resistance surveillance and vector control. We used the 454 GS FLX system and generated expressed sequence tag (EST) databases of various life stages of An. sinensis, and we determined the transcriptional differences between deltamethrin resistant and susceptible mosquitoes.ResultsThe 454 GS FLX transcriptome sequencing yielded a total of 624,559 reads (average length of 290 bp) with the pooled An. sinensis mosquitoes across various development stages. The de novo assembly generated 33,411 contigs with average length of 493 bp. A total of 8,057 ESTs were generated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. A total of 2,131 ESTs were differentially expressed between deltamethrin resistant and susceptible mosquitoes collected from the same field site in Jiangsu, China. Among these differentially expressed ESTs, a total of 294 pathways were mapped to the KEGG database, with the predominant ESTs belonging to metabolic pathways. Furthermore, a total of 2,408 microsatellites and 15,496 single nucleotide polymorphisms (SNPs) were identified.ConclusionsThe annotated EST and transcriptome databases provide a valuable genomic resource for further genetic studies of this important malaria vector species. The differentially expressed ESTs associated with insecticide resistance identified in this study lay an important foundation for further functional analysis. The identified microsatellite and SNP markers will provide useful tools for future population genetic and comparative genomic analyses of malaria vectors.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-448) contains supplementary material, which is available to authorized users.

Transcriptome analysis for leaves of five chemical types in Cinnamomum camphora

Camphor tree (Cinnamomum camphora) is a representative species in Lauraceae family, and can be subdivided into five types: linalool, camphor, cineol, iso-nerolidol and borneol. In this paper, the leaves transcriptomes of Cinnamomum camphora were sequenced with the platform of Illumina HiSeq™ 2000. Based on the GO (Gene Ontology), COG (Clusters of Orthologous Groups), and KEGG (Kyoto Encyclopedia of Genes and Genomes) database, the function classification, pathway annotation, and the coding sequence prediction of all-Unigenes were carried out. 156 278 Unigenes with an average length of 584 bp and N50 (N50 value is defined as the Unigene length where half the assembly is represented by Unigenes of this size or longer) of 1 023 bp were generated by de novo assembly. A total of 5 5955 Unigenes (35.80%) were annotated through similarity comparison, in which 24 717 and 21 806 Unigenes were assigned into GO and COG, respectively. By searching KEGG database, 3 350 Unigenes were involved in biosynthesis of secondary metabolites, in which 424 Unigenes were involved in monoterpenoids, diterpenoids, sesquiterpenoids, and terpenoid backbone biosynthesis. The analysis of monoterpenoids biosynthesis pathway showed that 9 Unigenes likely encode (+)-linalool synthase, and their expression levels were higher in linalool type but lower in cineole type. This study provides a foundation for further characterizing the functional genes in C. camphora.

Screening of differentially expressed genes and gene pathways in hepatitis C virus 1b type nonstructural protein 4B stably expressed L02 cell line

To screen differentially expressed genes and gene pathways in L02 cell line stably expressing hepatitis C virus (HCV) Ib type nonstructural protein 4B (NS4B) mediated by lentiviral system, and to provide a basis for further research of molecular biological mechanism of NS4B gene in chronic hepatitis C and hepatocarcinogenesis. NS4B stably overexpressed L02 cell line and negative control stable L02 cell line, designated as L02-NS4B and L02-mkate2 respectively, were resurrected and amplified in vitro. The differentially expressed genes between L02-NS4B and L02-mkate2 were determined by gene expression microarray from Human Gene 1.0ST. The significant pathways of the differential genes were selected by the Fisher's exact test and χ2 test according to kyoto encyclopedia of genes and genomes (KEGG) database. The differential expression levels of 5 selected genes including protein kinase C delta binding protein (PRKCDBP), tumor protein p53 (TP53), v-akt murine thymoma viral oncogene homolog 1 (AKT1), baculoviral IAP repeat containing 3 (BIRC3) and B-cell lymphoma 2-like1 (BCL2L1) from cDNA microarray data were further verified by real-time quantitative polymerase chain reaction (real-time QPCR). Between L02-NS4B and L02-mkate2, the genes with flurescence intensity ratio >1.2 or <0.8 were considered as differentially expressed genes. A total of 2 682 differentially expressed genes in the known 28 869 human genes were detected in L02-NS4B, 1 446 genes were upregulated and 1 236 genes were downregulated. A total of 41 involved pathways of up-regulated differential genes were identified by KEGG database, mainly including apoptosis, extracellular matrix receptor interaction, cell cycle, pathways in cancer and Toll-like receptor signaling pathway; and 20 involved pathways of down-regulated differential genes were identified, mainly including pathways in cancer, Wnt signaling pathway and cell cycle pathway. Of the 5 upregulated genes selected from cDNA microarray data, 3 genes showed the same differential expression pattern by real-time QPCR as that shown in cDNA microarray data, namely AKT1, BIRC3 and BCL2L1. The confirmation rate of real-time QPCR was 60%. HCVNS4B can up-regulate or down-regulate the expression of many genes in L02 cells, thus affecting multiple signaling pathways relevant to cell apoptosis, cell cycle and carcinogenesis.

Validation and target gene screening of hsa-miR-205 in lung squamous cell carcinoma

Background Lung cancers are classified as squamous cell carcinoma (SQ), adenocarcinoma (AC) and small cell lung carcinoma (SCLC). SQ is the major subtype of lung cancer. Currently, there are no targeted therapies for SQ due to lack of understanding its driving oncogenes. In this study, we validated an SQ specific biomarker hsa-miR-205 in Chinese patients with lung cancer and screened its candidate target genes for further functional studies to enrich knowledge in SQ target therapies. Methods Quantitative reverse-transcription PCR (quantitative RT-PCR) was performed on 197 macro-dissected (cancerous cells &gt;75%) surgical lung tissues (45 SQ, 44 AC, 54 SCLC and 54 adjacent normal tissues) to validate the expression profiles of miR-205. Furthermore, the targets of this microRNA were predicted through the gateway miRecords and mapped to lung cancer-associated pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Then quantitative RT-PCR was performed on an independent cohort of 44 snap-frozen surgical lung tissues to concurrently assess the expression profiles of miR-205 and its 52 putative targeted genes. Results MicroRNA-205 yielded high diagnostic accuracy in discriminating SQ from AC with an area under the curve (AUC) of 0.985, and discriminating SQ from SCLC with an AUC of 0.978 in formalin-fixed paraffin-embedded (FFPE) surgical lung tissues. Predicted targets of miR-205 were associated with 52 key members of lung cancer signaling pathways. Ten target genes (ACSL1, AXIN2, CACNA2D2, FOXO3, PPP1R3A, PRKAG3, RUNX1, SMAD4, STK3 and TBL1XR1) were significantly down-regulated in SQ and had a strong negative correlation with miR-205, while one target gene (CDH3) was up-regulated in SQ and exhibited a strong positive correlation with miR-205. Conclusions We confirmed the high diagnostic accuracy of miR-205 in discriminating SQ from AC and SCLC in Chinese patients. Moreover, we identified 11 significant target genes of miR-205 which could be used for further functional studies as the basis for the development of SQ targeted therapies.

The Analysis of microRNA Expression Profiling for Coronary Artery Disease

Objectives: To investigate the underlying molecular mechanisms of coronary artery disease (CAD) using microarray expression profiles. Methods: The microRNA (miRNA) expression-profiling dataset GSE28858 was obtained from the Gene Expression Omnibus database, including 24 samples from 12 patients with CAD and 12 age- and sex-matched healthy controls. Differentially expressed miRNAs were identified with false discovery rate (FDR) = 1% by the SAM (Significant Analysis of Microarray) algorithm. The target genes of selected differentials expressed miRNAs that were not only related to CAD, but were also in two databases (TargetScan, miRanda). Then, the interactive objects of selected target genes were predicted using the STRING database to construct an interaction network (confidence score = 0.4). These target genes and interactive objects were put into the KEGG (Kyoto Encyclopedia of Genes and Genomes) database, and the significant signaling pathway was obtained by hypergeometric function enrichment analysis (p < 0.05). Results: MiRNA-526b was the only differentially expressed miRNA that was upregulated in patients with CAD (FDR = 1%). Toll-like receptor 4 (TLR4) was the target gene of miRNA-526b that occurred with the highest frequency. The objects that interacted with TLR4 were predicted using the STRING database and the interaction network was obtained. The vascular endothelial growth factor (VEGF) signaling pathway was the only selected significant pathway related with CAD in the interaction network (p < 0.05). Conclusion: The miRNA-526b is significantly upregulated in patients with CAD and the target gene of miRNA-526b participates in the VEGF signaling pathway. Whether or not the miRNA-526b can be used as a biomarker remains to be elucidated in a larger prospective study.

Identification of a set of miRNAs differentially expressed in transiently TIA-depleted HeLa cells by genome-wide profiling

BackgroundT-cell intracellular antigen (TIA) proteins function as regulators of cell homeostasis. These proteins control gene expression globally at multiple levels in response to dynamic regulatory changes and environmental stresses. Herein we identified a micro(mi)RNA signature associated to transiently TIA-depleted HeLa cells and analyzed the potential role of miRNAs combining genome-wide analysis data on mRNA and miRNA profiles.ResultsUsing high-throughput miRNA expression profiling, transient depletion of TIA-proteins in HeLa cells was observed to promote significant and reproducible changes affecting to a pool of up-regulated miRNAs involving miR-30b-3p, miR125a-3p, miR-193a-5p, miR-197-3p, miR-203a, miR-210, miR-371-5p, miR-373-5p, miR-483-5p, miR-492, miR-498, miR-503-5p, miR-572, miR-586, miR-612, miR-615-3p, miR-623, miR-625-5p, miR-629-5p, miR-638, miR-658, miR-663a, miR-671-5p, miR-769-3p and miR-744-5p. Some up-regulated and unchanged miRNAs were validated and previous results confirmed by reverse transcription and real time PCR. By target prediction of the miRNAs and combined analysis of the genome-wide expression profiles identified in TIA-depleted HeLa cells, we detected connections between up-regulated miRNAs and potential target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis suggest that target genes are related with biological processes associated to the regulation of DNA-dependent transcription, signal transduction and multicellular organismal development as well as with the enrichment of pathways involved in cancer, focal adhesion, regulation of actin cytoskeleton, endocytosis and MAPK and Wnt signaling pathways, respectively. When the collection of experimentally defined differentially expressed genes in TIA-depleted HeLa cells was intersected with potential target genes only 7 out of 68 (10%) up- and 71 out of 328 (22%) down-regulated genes were shared. GO and KEGG database analyses showed that the enrichment categories of biological processes and cellular pathways were related with innate immune response, signal transduction, response to interleukin-1, glomerular basement membrane development as well as neuroactive ligand-receptor interaction, endocytosis, lysosomes and apoptosis, respectively.ConclusionAll this considered, these observations suggest that individual miRNAs could act as potential mediators of the epigenetic switch linking transcriptomic dynamics and cell phenotypes mediated by TIA proteins.

Retraction Notice: Microarray and synchronization of neuronal differentiation with pathway changes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) databank in nerve growth factor-treated PC12 cells

The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database creates networks from interrelations between molecular biology and underlying chemical elements. This allows for analysis of biologic networks, genomic information, and higher-order functional information at a systems level. We performed microarray experiments and used the KEGG database, systems biology analysis, and annotation of pathway function to study nerve growth factor (NGF)-induced differentiation of PC12 cells. Cells were cultured to 70%-80% confluence, treated with NGF for 1 or 3 hours (h), and RNA was extracted. Stage 1 data analysis involved analysis of variance (ANOVA), and stage 2 involved cluster analysis and heat map generation. We identified 2020 NGF-induced PC12 genes (1038 at 1 h and 1554 at 3 h). Results showed changes in gene expression over time. We compared these genes with 6035 genes from the KEGG database. Cross-matching resulted in 830 genes. Among these, we identified 395 altered genes (155 at 1 h and 301 at 3 h; 2-fold increase from 1 h to 3 h). We identified 191 biologic pathways in the KEGG database; the top 15 showed correlations with neuronal differentiation (mitogen-activated protein kinase [MAPK] pathway: 35 genes at 1 h, 54 genes at 3 h; genes associated with axonal guidance: 12 at 1 h, 26 at 3 h; Wnt pathway: 16 at 1 h, 25 at 3 h; neurotrophin pathway: 4 at 1 h, 14 at 3 h). Thus, we identified changes in neuronal differentiation pathways with the KEGG database, which were synchronized with NGF-induced differentiation.

Using the KEGG database resource.

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding the functions and utilities of cells and organisms from both high-level and genomic perspectives. It is a self-sufficient, integrated resource consisting of genomic, chemical, and network information, with cross-references to numerous outside databases. The genomic and chemical information is a complete set of building blocks (genes and molecules) and the network information includes molecular wiring diagrams (interaction/reaction networks) and hierarchical classifications (relation networks) to represent high-level functions. This unit describes protocols for using KEGG, focusing on molecular network information in KEGG PATHWAY, KEGG BRITE, and KEGG MODULE, perturbed molecular networks in KEGG DISEASE and KEGG DRUG, molecular building block information in KEGG GENES and KEGG LIGAND, and a mechanism for linking genomes to molecular networks in KEGG ORTHOLOGY (KO). All of these many protocols enable the user to take advantage of the full breadth of the functionality provided by KEGG.

Mo1534 Association Between Telomere Length and Risk of Cirrhosis in Patients With Chronic Hepatitis B

Background and Aim: To screen differentially expressed genes and MicroRNAs hoping bring us a new target spot to accurate diagnosis and effective therapy in gene and MicroRNA level of alcoholic liver disease(ALD).Methods: The total RNA of peripheral blood was extracted from four groups of three subjects.And all patients signed the informed consents. Microarrays were utilized to detect differentially expressed genes and MicroRNAs. According to gene values, significance level (p values) and false discovery rate with a random variance model, combining the GO and KEGG database, node genes and key MicroRNAs in network were obtained and analyzed.Results: A total of 878 differentially expressed genes and 26 MicroRNAs were discovered. Not all of these genes have biological effects on the development of ALD. By combining the gene ontology (GO) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 16 significantly different pathways were found, where 31 corresponding genes participated in.Calculating betweenness centrality of each gene in network, which can describe the degree of importance of the nodes in the whole net. In co-expression network of genes, the node genes modulating the network were ACSF3, FZD5, LOC727987 and C1orf222. And in MicroRNA-Gene network the key MicroRNAs were hsa-miR-570, hsa-miR-122, hsa-miR-34b, hsa-miR-29c, hsa-miR-922 and hsa-miR-185 they negatively regulated about 79 genes locate their downstream.Conclusions: In the course of the ALD, we found 4 differentially expressed node genes in network and analyzed Acyl-coenzyme A synthetase-3 (ACSF3) , the maximal betweenness centrality in the entire gene-modulating network was 0.102935, indicating its controlling capability and significance level. Continuous up-regulation of ACSF3 maintains transcriptional activation and subsequently strengthens the binding of ACSF3 to thioester and CoA to activate fatty acids, which results in the irreversible advancement of ALD from hepatitis to cirrhosis. The gene values of Frizzled-5(FZD5) in alcoholic hepatitis and cirrhosis were clearly downregulated. The second highest value of betweenness centrality in the entire gene-modulating network was 0.087. A possible mechanism may be that continuous down-regulation of FZD5 during advancement of alcoholic hepatitis to cirrhosis decreased gene activities and syntheses of multi-transmembrane transport proteins. This reduced the number of β-catenin molecules in hepatocytes and therefore promoted hepatocyte apoptosis. The other two genes' functions were unknown. And the 6 key MicroRNAs perhaps controlled numerous biology functions such as immune response, activity of cancer gene, inflammatory mediated response, cell cycle, glutathione metabolism. Maybe the discovery will provide valuable directions to diagnosis and treatment of ALD.

771 TLR3-DEPENDENT IMMUNOLOGICAL PROPERTIES OF LIVER CELLS ARE CONTROLLED BY ANTI-INFLAMMATORY CYTOKINES THROUGH MODULATION OF MIR-155 EXPRESSION

Background and Aim: To screen differentially expressed genes and MicroRNAs hoping bring us a new target spot to accurate diagnosis and effective therapy in gene and MicroRNA level of alcoholic liver disease(ALD).Methods: The total RNA of peripheral blood was extracted from four groups of three subjects.And all patients signed the informed consents. Microarrays were utilized to detect differentially expressed genes and MicroRNAs. According to gene values, significance level (p values) and false discovery rate with a random variance model, combining the GO and KEGG database, node genes and key MicroRNAs in network were obtained and analyzed.Results: A total of 878 differentially expressed genes and 26 MicroRNAs were discovered. Not all of these genes have biological effects on the development of ALD. By combining the gene ontology (GO) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 16 significantly different pathways were found, where 31 corresponding genes participated in.Calculating betweenness centrality of each gene in network, which can describe the degree of importance of the nodes in the whole net. In co-expression network of genes, the node genes modulating the network were ACSF3, FZD5, LOC727987 and C1orf222. And in MicroRNA-Gene network the key MicroRNAs were hsa-miR-570, hsa-miR-122, hsa-miR-34b, hsa-miR-29c, hsa-miR-922 and hsa-miR-185 they negatively regulated about 79 genes locate their downstream.Conclusions: In the course of the ALD, we found 4 differentially expressed node genes in network and analyzed Acyl-coenzyme A synthetase-3 (ACSF3) , the maximal betweenness centrality in the entire gene-modulating network was 0.102935, indicating its controlling capability and significance level. Continuous up-regulation of ACSF3 maintains transcriptional activation and subsequently strengthens the binding of ACSF3 to thioester and CoA to activate fatty acids, which results in the irreversible advancement of ALD from hepatitis to cirrhosis. The gene values of Frizzled-5(FZD5) in alcoholic hepatitis and cirrhosis were clearly downregulated. The second highest value of betweenness centrality in the entire gene-modulating network was 0.087. A possible mechanism may be that continuous down-regulation of FZD5 during advancement of alcoholic hepatitis to cirrhosis decreased gene activities and syntheses of multi-transmembrane transport proteins. This reduced the number of β-catenin molecules in hepatocytes and therefore promoted hepatocyte apoptosis. The other two genes' functions were unknown. And the 6 key MicroRNAs perhaps controlled numerous biology functions such as immune response, activity of cancer gene, inflammatory mediated response, cell cycle, glutathione metabolism. Maybe the discovery will provide valuable directions to diagnosis and treatment of ALD.

Analysis of Transcriptome Differences between Resistant and Susceptible Strains of the Citrus Red Mite Panonychus citri (Acari: Tetranychidae)

BackgroundThe citrus red mite is a worldwide citrus pest and a common sensitizing allergen of asthma and rhinitis. It has developed strong resistance to many registered acaricides, However, the molecular mechanisms of resistance remain unknown. we therefore used next generation sequencing technology to investigate the global transcriptomes between resistant strains and susceptible strains.ResultsWe obtained 34,159, 30,466 and 32,217 unigenes by assembling the SS reads, RS reads and SS&RS reads respectively. There are total 17,581 annotated unigenes from SS&RS reads by BLAST searching databases of nr, the Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) with an E-value ≤ 1e-5, in which 7,075 unigenes were annotated in the COG database, 12, 712 unigenes were found in the KEGG database and 3,812 unigenes were assigned to Gene ontology (GO). Moreover, 2,701 unigenes were judged to be the differentially expressed genes (DEGs) based on the uniquely mapped reads. There are 219 pathways in all annotated unigenes and 198 pathways in DEGs that mapped to the KEGG database. We identified 211 metabolism genes and target genes related to general insecticide resistance such as P450 and Cytochrome b, and further compared their differences between RS and SS. Meanwhile, we identified 105 and 194 genes related to growth and reproduction, respectively, based on the mode of action of Hexythiazox. After further analyses, we found variation in sequences but not in gene expression related to mite growth and reproduction between different strains.ConclusionTo our knowledge, this is the first comparative transcriptome study to discover candidate genes involved in phytophagous mite resistance. This study identified differential unigenes related to general pesticide resistance and organism growth and reproduction in P. citri. The assembled, annotated transcriptomes provide a valuable genomic resource for further understanding the molecular basis of resistance mechanisms.

Comparative Study of different msDNA (multicopy single-stranded DNA) structures and phylogenetic comparison of reverse transcriptases (RTs): evidence for vertical inheritance.

The multi-copy single-stranded DNA (msDNA) is yielded by the action of reverse transcriptase of retro-element in a wide range of pathogenic bacteria. Upon this phenomenon, it has been shown that msDNA is only produced by Eubacteria because many Eubacteria species contained reverse transcriptase in their special retro-element. We have screened around 111 Archaea at KEGG (Kyoto Encyclopedia of Genes and Genomes) database available at genome net server and observed three Methanosarcina species (M.acetivorans, M.barkeri and M.mazei), which also contained reverse transcriptase in their genome sequences. This observation of reverse transcriptase in Archaea raises questions regarding the origin of this enzyme. The evolutionary relationship between these two domains of life (Eubacteria and Archaea) hinges upon the phenomenon of retrons. Interestingly, the evolutionary trees based on the reverse transcriptases (RTs) and 16S ribosomal RNAs point out that all the Eubacteria RTs were descended from Archaea RTs during their evolutionary times. In addition, we also have shown some significant structural features among the newly identified msDNA-Yf79 in Yersinia frederiksenii with other of its related msDNAs (msDNA-St85, msDNA-Vc95, msDNA-Vp96, msDNA-Ec78 and msDNA-Ec83) from pathogenic bacteria. Together the degree of sequence conservation among these msDNAs, the evolutionary trees and the distribution of these ret (reverse transcriptase) genes suggest a possible evolutionary scenario. The single common ancestor of the organisms of Eubacteria and Archaea subgroups probably achieved this ret gene during their evolution through the vertical descent rather than the horizontal transformations followed by integration into this organism genome by a mechanism related to phage recognition and/or transposition.

Integrative analysis of cancer pathway progression and coherence

We analyzed the cancer pathways in the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. The database provides a collective of signaling pathway members involved in cancer progression. However, the KEGG cancer pathways, unlike signaling pathways, have not been analyzed extensively with gene expression and mutation data. We transformed the colorectal cancer pathway into discrete X and Y scales and analyzed the relative expression levels of adenoma and carcinoma samples as well as the distribution of mutation targets. The X scale corresponds to the downstream location in a pathway, whereas the Y scale corresponds to the stage of the tumor. The gene expression values of the early stage pathway members are significantly higher than of the rest of the pathway members in colorectal adenoma tissues. The colorectal cancer pathway shows some degree of coherence in the carcinoma samples. The correlated gene pairs responsible for the coherence of the colorectal cancer pathway in the carcinoma samples are supported, in part, by the literature and may suggest novel regulatory associations. Finally, there are more mutation targets in the nucleus as well as the late tumor stages of the KEGG colorectal cancer pathway.

Biological Pathway Extension Using Microarray Gene Expression Data

Biological pathways are known as collections of knowledge of certain biological processes. Although knowledge about a pathway is quite significant to further analysis, it covers only tiny portion of genes that exists. In this paper, we suggest a model to extend each individual pathway using a microarray expression data based on the known knowledge about the pathway. We take the Rosetta compendium dataset to extend pathways of Saccharomyces cerevisiae obtained from KEGG (Kyoto Encyclopedia of genes and genomes) database. Before applying our model, we verify the underlying assumption that microarray data reflect the interactive knowledge from pathway, and we evaluate our scoring system by introducing performance function. In the last step, we validate proposed candidates with the help of another type of biological information. We introduced a pathway extending model using its intrinsic structure and microarray expression data. The model provides the suitable candidate genes for each single biological pathway to extend it.

A network perspective on the topological importance of enzymes and their phylogenetic conservation.

BackgroundA metabolic network is the sum of all chemical transformations or reactions in the cell, with the metabolites being interconnected by enzyme-catalyzed reactions. Many enzymes exist in numerous species while others occur only in a few. We ask if there are relationships between the phylogenetic profile of an enzyme, or the number of different bacterial species that contain it, and its topological importance in the metabolic network. Our null hypothesis is that phylogenetic profile is independent of topological importance. To test our null hypothesis we constructed an enzyme network from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. We calculated three network indices of topological importance: the degree or the number of connections of a network node; closeness centrality, which measures how close a node is to others; and betweenness centrality measuring how frequently a node appears on all shortest paths between two other nodes.ResultsEnzyme phylogenetic profile correlates best with betweenness centrality and also quite closely with degree, but poorly with closeness centrality. Both betweenness and closeness centralities are non-local measures of topological importance and it is intriguing that they have contrasting power of predicting phylogenetic profile in bacterial species. We speculate that redundancy in an enzyme network may be reflected by betweenness centrality but not by closeness centrality. We also discuss factors influencing the correlation between phylogenetic profile and topological importance.ConclusionOur analysis falsifies the hypothesis that phylogenetic profile of enzymes is independent of enzyme network importance. Our results show that phylogenetic profile correlates better with degree and betweenness centrality, but less so with closeness centrality. Enzymes that occur in many bacterial species tend to be those that have high network importance. We speculate that this phenomenon originates in mechanisms driving network evolution. Closeness centrality reflects phylogenetic profile poorly. This is because metabolic networks often consist of distinct functional modules and some are not in the centre of the network. Enzymes in these peripheral parts of a network might be important for cell survival and should therefore occur in many bacterial species. They are, however, distant from other enzymes in the same network.

Oligosaccharides, neoglycoproteins and humanized plastics: their biocatalytic synthesis and possible medical applications

Glycobiology has become one of the fastest growing branches of the biological sciences. Glycomics, which is the study of an organism's entire array of oligosaccharides, is now emerging as the third informatics wave after genomics and proteomics. For example, it is possible to see this progress in the KEGG (Kyoto Encyclopedia of Genes and Genomes) database (http://www.genome.jp/kegg/pathway/map/map01110.html). The interest in this area stems from the realization that carbohydrates, especially oligosaccharides, and their interactions with proteins, play diverse informative roles in all organisms, and that more than half of all proteins are glycosylated. When the biological and pharmaceutical importance of glycoconjugates is considered, it is surprising how little glycobiotechnology has developed. This review reports the latest developments in the biocatalytic synthesis of oligosaccharides and glycoconjugates, with special attention paid to the glycosyltransferase approach. The second part of the review takes the 'conceptual approach' and covers possible medical applications of synthesized glycoconjugates. Various new examples of the conjugation of glyco-informative saccharide sequence to known pharmaceuticals or biomaterials are cited.

PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database

BackgroundEqually important and challenging as genome annotation, is the subsequent classification of predicted genes into their respective pathways. The Kyoto Encyclopedia of Genes and Genomes (KEGG) represents a database consisting of known genes and their respective biochemical functionalities. Although accessible online, analyses of multiple genes are time consuming and are not suitable for analyzing data sets that are proprietary.ResultsPresented here is a new software solution that utilizes the KEGG online database for pathway mapping of partial and whole prokaryotic genomes. PathwayVoyager retrieves user-defined subsets of the KEGG database and stores the data as local, blast-formatted databases. Previously selected datasets can be re-used, reducing run-time significantly. Whole or partial genomes can be automatically analyzed using NCBI's BlastP algorithm and ORFs with similarities below the user-defined threshold will be marked on pathway maps. Multiple gene hits are sorted by similarity. Since no sequence information is transmitted over the Internet, PathwayVoyager is an ideal solution for pathway mapping and reconstruction of confidential DNA sequence data.ConclusionPathwayVoyager represents an alternative approach to many already existing, more complex pathway reconstructions software solutions. This software does not require any dedicated hardware or software and is flexible and straightforward to use. It is ideally suited for environments where analyses on variable datasets are desired.

The KEGG databases at GenomeNet.

The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the primary database resource of the Japanese GenomeNet service (http://www.genome.ad.jp/) for understanding higher order functional meanings and utilities of the cell or the organism from its genome information. KEGG consists of the PATHWAY database for the computerized knowledge on molecular interaction networks such as pathways and complexes, the GENES database for the information about genes and proteins generated by genome sequencing projects, and the LIGAND database for the information about chemical compounds and chemical reactions that are relevant to cellular processes. In addition to these three main databases, limited amounts of experimental data for microarray gene expression profiles and yeast two-hybrid systems are stored in the EXPRESSION and BRITE databases, respectively. Furthermore, a new database, named SSDB, is available for exploring the universe of all protein coding genes in the complete genomes and for identifying functional links and ortholog groups. The data objects in the KEGG databases are all represented as graphs and various computational methods are developed to detect graph features that can be related to biological functions. For example, the correlated clusters are graph similarities which can be used to predict a set of genes coding for a pathway or a complex, as summarized in the ortholog group tables, and the cliques in the SSDB graph are used to annotate genes. The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/).

KEGG: Kyoto Encyclopedia of Genes and Genomes

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).

KEGG: Kyoto Encyclopedia of Genes and Genomes.

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).