01472nas a2200205 4500008004100000245009600041210006900137300001300206490000700219520083200226653001601058653001201074653000901086100001901095700001301114700002001127700002401147700002001171856007501191 2009 eng d00aSNOW, a web-based tool for the statistical analysis of protein-protein interaction networks0 aSNOW a webbased tool for the statistical analysis of proteinprot aW109-1140 v373 a

Understanding the structure and the dynamics of the complex intercellular network of interactions that contributes to the structure and function of a living cell is one of the main challenges of today’s biology. SNOW inputs a collection of protein (or gene) identifiers and, by using the interactome as scaffold, draws the connections among them, calculates several relevant network parameters and, as a novelty among the rest of tools of its class, it estimates their statistical significance. The parameters calculated for each node are: connectivity, betweenness and clustering coefficient. It also calculates the number of components, number of bicomponents and articulation points. An interactive network viewer is also available to explore the resulting network. SNOW is available at http://snow.bioinfo.cipf.es.

10ainteractome10anetwork10asnow1 aMinguez, Pablo1 aGotz, S.1 aMontaner, David1 aAl-Shahrour, Fatima1 aDopazo, Joaquin uhttp://nar.oxfordjournals.org/content/early/2009/05/19/nar.gkp402.full01483nas a2200133 4500008004100000245007800041210006900119300001100188490000900199520100700208100001501215700001301230856010601243 2008 eng d00aBlast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics0 aBlast2GO A Comprehensive Suite for Functional Analysis in Plant  a6198320 v20083 a

Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. Blast2GO is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use.

1 aConesa, A.1 aGotz, S. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1848357201778nas a2200229 4500008004100000245010300041210006900144300001100213490000700224520087500231653007101106653013601177100001501313700001201328700002201340700001801362700001301380700001701393700001701410700001501427856010601442 2008 eng d00aDirect functional assessment of the composite phenotype through multivariate projection strategies0 aDirect functional assessment of the composite phenotype through  a373-830 v923 a

We present a novel approach for the analysis of transcriptomics data that integrates functional annotation of gene sets with expression values in a multivariate fashion, and directly assesses the relation of functional features to a multivariate space of response phenotypical variables. Multivariate projection methods are used to obtain new correlated variables for a set of genes that share a given function. These new functional variables are then related to the response variables of interest. The analysis of the principal directions of the multivariate regression allows for the identification of gene function features correlated with the phenotype. Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches.

10aBreast Neoplasms/genetics Computational Biology/*methods Databases10aGenetic Female Gene Expression Profiling/*statistics & numerical data Humans Mathematical Computing Multivariate Analysis Phenotype1 aConesa, A.1 aBro, R.1 aGarcia-Garcia, F.1 aPrats, J., M.1 aGotz, S.1 aKjeldahl, K.1 aMontaner, D.1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1865288803856nas a2200385 4500008004100000245011000041210006900151300000700220490000600227520253000233653016602763653002902929653009302958100001403051700001503065700002203080700001503102700001403117700001503131700001303146700001503159700001403174700001503188700002103203700001303224700001403237700001503251700001703266700001903283700001503302700001603317700001703333700001403350856010603364 2007 eng d00aAnalysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance0 aAnalysis of 13000 unique Citrus clusters associated with fruit q a310 v83 aBACKGROUND: Improvement of Citrus, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity. RESULTS: A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (Citrus clementina and C. sinensis) and rootstocks (C. reshni, and C. sinenis x Poncirus trifoliata) differing in fruit quality, resistance to abscission, and tolerance to salinity. The goal of this work was to provide a large expressed sequence tag (EST) collection enriched with transcripts related to these well appreciated agronomical traits. Towards this end, more than 54000 ESTs derived from these libraries were analyzed and annotated. Assembly of 52626 useful sequences generated 15664 putative transcription units distributed in 7120 contigs, and 8544 singletons. BLAST annotation produced significant hits for more than 80% of the hypothetical transcription units and suggested that 647 of these might be Citrus specific unigenes. The unigene set, composed of 13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains CONCLUSION: Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus and also the occurrence of both gene duplication events and increased number of genes for specific pathways. In addition, phylogenetic analysis performed on the ammonium transporter family and glycosyl transferase family 20 suggested the existence of Citrus paralogs. Analysis of the Citrus gene space showed that the most important metabolic pathways known to affect fruit quality were represented in the unigene set. Overall, the similarity analyses indicated that the sequences of the genes belonging to these varieties and rootstocks were essentially identical, suggesting that the differential behaviour of these species cannot be attributed to major sequence divergences. This Citrus EST assembly contributes both crucial information to discover genes of agronomical interest and tools for genetic and genomic analyses, such as the development of new markers and microarrays.10aAcclimatization/*genetics Amino Acid Motifs Citrus/*genetics Cluster Analysis Expressed Sequence Tags Fruit/genetics Gene Duplication *Gene Expression Regulation10aPlant Gene Library Genes10aPlant Genomics Molecular Sequence Data Multigene Family Phylogeny *Salts/adverse effects1 aTerol, J.1 aConesa, A.1 aColmenero, J., M.1 aCercos, M.1 aTadeo, F.1 aAgusti, J.1 aAlos, E.1 aAndres, F.1 aSoler, G.1 aBrumos, J.1 aIglesias, D., J.1 aGotz, S.1 aLegaz, F.1 aArgout, X.1 aCourtois, B.1 aOllitrault, P.1 aDossat, C.1 aWincker, P.1 aMorillon, R.1 aTalon, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1725432702376nas a2200229 4500008004100000245009300041210006900134300001200203490000800215520165600223653001501879100001701894700001301911700001501924700001801939700001701957700001901974700001801993700001502011700001402026856010602040 2006 eng d00aBlast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis0 aBlast2GO goes grid developing a gridenabled prototype for functi a194-2040 v1203 a

The vast amount in complexity of data generated in Genomic Research implies that new dedicated and powerful computational tools need to be developed to meet their analysis requirements. Blast2GO (B2G) is a bioinformatics tool for Gene Ontology-based DNA or protein sequence annotation and function-based data mining. The application has been developed with the aim of affering an easy-to-use tool for functional genomics research. Typical B2G users are middle size genomics labs carrying out sequencing, ETS and microarray projects, handling datasets up to several thousand sequences. In the current version of B2G. The power and analytical potential of both annotation and function data-mining is somehow restricted to the computational power behind each particular installation. In order to be able to offer the possibility of an enhanced computational capacity within this bioinformatics application, a Grid component is being developed. A prototype has been conceived for the particular problem of speeding up the Blast searches to obtain fast results for large datasets. Many efforts have been done in the literature concerning the speeding up of Blast searches, but few of them deal with the use of large heterogeneous production Grid Infrastructures. These are the infrastructures that could reach the largest number of resources and the best load balancing for data access. The Grid Service under development will analyse requests based on the number of sequences, splitting them accordingly to the available resources. Lower-level computation will be performed through MPIBLAST. The software architecture is based on the WSRF standard.

10ababelomics1 aAparicio, G.1 aGotz, S.1 aConesa, A.1 aSegrelles, D.1 aBlanquer, I.1 aGarcia, J., M.1 aHernandez, V.1 aRobles, M.1 aTalon, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1682313801401nas a2200193 4500008004100000245010600041210006900147300001100216490000700227520075600234653001500990100001501005700001301020700002501033700001401058700001401072700001501086856010601101 2005 eng d00aBlast2GO: a universal tool for annotation, visualization and analysis in functional genomics research0 aBlast2GO a universal tool for annotation visualization and analy a3674-60 v213 a

SUMMARY: We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. AVAILABILITY: Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL: http://www.blast2go.de -> Evaluation.

10ababelomics1 aConesa, A.1 aGotz, S.1 aGarcia-Gomez, J., M.1 aTerol, J.1 aTalon, M.1 aRobles, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16081474