02445nas a2200469 4500008004100000022001400041245008300055210006900138260001600207300001400223490000700237520108700244653001501331653002101346653002201367653001601389653002101405653000801426653001201434653002001446653002001466100002001486700002401506700002901530700003101559700001701590700002401607700002301631700002201654700002401676700002101700700001801721700002201739700001901761700003601780700002301816700002301839700002001862700002001882700002001902856005301922 2015 eng d a1362-496200aBabelomics 5.0: functional interpretation for new generations of genomic data.0 aBabelomics 50 functional interpretation for new generations of g c2015 Apr 20 aW117-W1210 v433 aBabelomics has been running for more than one decade offering a user-friendly interface for the functional analysis of gene expression and genomic data. Here we present its fifth release, which includes support for Next Generation Sequencing data including gene expression (RNA-seq), exome or genome resequencing. Babelomics has simplified its interface, being now more intuitive. Improved visualization options, such as a genome viewer as well as an interactive network viewer, have been implemented. New technical enhancements at both, client and server sides, makes the user experience faster and more dynamic. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a variety of tests for different experimental designs and (iii) different enrichment and network analysis algorithms for the interpretation of the results of such tests in the proper functional context. In addition to the public server, local copies of Babelomics can be downloaded and installed. Babelomics is freely available at: http://www.babelomics.org.10ababelomics10adata integration10agene set analysis10ainteractome10anetwork analysis10aNGS10aRNA-seq10aSystems biology10atranscriptomics1 aAlonso, Roberto1 aSalavert, Francisco1 aGarcia-Garcia, Francisco1 aCarbonell-Caballero, José1 aBleda, Marta1 aGarcía-Alonso, Luz1 aSanchis-Juan, Alba1 aPerez-Gil, Daniel1 aMarin-Garcia, Pablo1 aSánchez, Rubén1 aCubuk, Cankut1 aHidalgo, Marta, R1 aAmadoz, Alicia1 aHernansaiz-Ballesteros, Rosa, D1 aAlemán, Alejandro1 aTárraga, Joaquín1 aMontaner, David1 aMedina, Ignacio1 aDopazo, Joaquin uhttp://nar.oxfordjournals.org/content/43/W1/W11702548nas a2200373 4500008004100000022001400041245009200055210006900147260000900216300001000225490000600235520144500241653001501686653001601701653000801717653001901725100002301744700001901767700002601786700002501812700002601837700002001863700002001883700002601903700002601929700002201955700001701977700003601994700002102030700002502051700003402076700001902110856004502129 2015 eng d a2045-232200aExome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease.0 aExome sequencing reveals a high genetic heterogeneity on familia c2015 a164730 v53 aHirschsprung disease (HSCR; OMIM 142623) is a developmental disorder characterized by aganglionosis along variable lengths of the distal gastrointestinal tract, which results in intestinal obstruction. Interactions among known HSCR genes and/or unknown disease susceptibility loci lead to variable severity of phenotype. Neither linkage nor genome-wide association studies have efficiently contributed to completely dissect the genetic pathways underlying this complex genetic disorder. We have performed whole exome sequencing of 16 HSCR patients from 8 unrelated families with SOLID platform. Variants shared by affected relatives were validated by Sanger sequencing. We searched for genes recurrently mutated across families. Only variations in the FAT3 gene were significantly enriched in five families. Within-family analysis identified compound heterozygotes for AHNAK and several genes (N = 23) with heterozygous variants that co-segregated with the phenotype. Network and pathway analyses facilitated the discovery of polygenic inheritance involving FAT3, HSCR known genes and their gene partners. Altogether, our approach has facilitated the detection of more than one damaging variant in biologically plausible genes that could jointly contribute to the phenotype. Our data may contribute to the understanding of the complex interactions that occur during enteric nervous system development and the etiopathology of familial HSCR.10ababelomics10aHirschprung10aNGS10aprioritization1 aLuzón-Toro, Berta1 aGui, Hongsheng1 aRuiz-Ferrer, Macarena1 aTang, Clara, Sze-Man1 aFernández, Raquel, M1 aSham, Pak-Chung1 aTorroglosa, Ana1 aTam, Paul, Kwong-Hang1 aEspino-Paisán, Laura1 aCherny, Stacey, S1 aBleda, Marta1 aEnguix-Riego, María, Del Valle1 aDopazo, Joaquín1 aAntiňolo, Guillermo1 aGarcia-Barceló, Maria-Mercè1 aBorrego, Salud uhttp://www.nature.com/articles/srep1647302554nas a2200361 4500008004100000245014100041210006900182260001600251300003100267490000700298520145100305653001501756653002001771653001501791653001001806653000801816653000901824100002001833700002101853700001701874700002101891700001801912700001601930700002301946700002901969700002701998700002002025700002302045700002002068700002002088700002102108856006302129 2010 eng d00aBabelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.0 aBabelomics an integrative platform for the analysis of transcrip c2010 May 16 aW210-W213. Featured in NAR0 v383 a
Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls and TDTs, and allows population stratification analysis and correction). All these genomic data analysis facilities are integrated and connected to multiple options for the functional interpretation of the experiments. Different methods of functional enrichment or gene set enrichment can be used to understand the functional basis of the experiment analyzed. Many sources of biological information, which include functional (GO, KEGG, Biocarta, Reactome, etc.), regulatory (Transfac, Jaspar, ORegAnno, miRNAs, etc.), text-mining or protein-protein interaction modules can be used for this purpose. Finally a tool for the de novo functional annotation of sequences has been included in the system. This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org.
10ababelomics10agene expression10agenotyping10agepas10aGSA10aGWAS1 aMedina, Ignacio1 aCarbonell, José1 aPulido, Luis1 aMadeira, Sara, C1 aGoetz, Stefan1 aConesa, Ana1 aTárraga, Joaquín1 aPascual-Montano, Alberto1 aNogales-Cadenas, Ruben1 aSantoyo, Javier1 aGarcía, Francisco1 aMarbà, Martina1 aMontaner, David1 aDopazo, Joaquín uhttp://nar.oxfordjournals.org/content/38/suppl_2/W210.full01598nas a2200145 4500008004100000245006200041210006200103300001100165490000700176520111100183653001501294653002201309100001501331856010601346 2009 eng d00aFormulating and testing hypotheses in functional genomics0 aFormulating and testing hypotheses in functional genomics a97-1070 v453 aOBJECTIVE: The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the results, relating the available genomic information to the hypotheses that originated the experiment. METHODS AND RESULTS: Initially, this interpretation has been made on a pre-selection of relevant genes, based on the experimental values, followed by the study of the enrichment in some functional properties. Nevertheless, functional enrichment methods, demonstrated to have a flaw: the first step of gene selection was too stringent given that the cooperation among genes was ignored. The assumption that modules of genes related by relevant biological properties (functionality, co-regulation, chromosomal location, etc.) are the real actors of the cell biology lead to the development of new procedures, inspired in systems biology criteria, generically known as gene-set methods. These methods have been successfully used to analyze transcriptomic and large-scale genotyping experiments as well as to test other different genome-scale hypothesis in other fields such as phylogenomics.
10ababelomics10agene set analysis1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1878965901715nas a2200265 4500008004100000245014300041210006900184300001300253490000700266520085600273653001501129653001301144653001101157653002701168653000801195100002001203700002001223700002101243700002601264700002101290700002301311700002401334700002001358856007101378 2009 eng d00aGene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies0 aGene setbased analysis of polymorphisms finding pathways or biol aW340-3440 v373 aGenome-wide association studies have become a popular strategy to find associations of genes to traits of interest. Despite the high-resolution available today to carry out genotyping studies, the success of its application in real studies has been limited by the testing strategy used. As an alternative to brute force solutions involving the use of very large cohorts, we propose the use of the Gene Set Analysis (GSA), a different analysis strategy based on testing the association of modules of functionally related genes. We show here how the Gene Set-based Analysis of Polymorphisms (GeSBAP), which is a simple implementation of the GSA strategy for the analysis of genome-wide association studies, provides a significant increase in the power testing for this type of studies. GeSBAP is freely available at http://bioinfo.cipf.es/gesbap/
10ababelomics10agene set10aGESBAP10apathway-based analysis10aSNP1 aMedina, Ignacio1 aMontaner, David1 aBonifaci, Núria1 aPujana, Miguel, Angel1 aCarbonell, José1 aTárraga, Joaquín1 aAl-Shahrour, Fatima1 aDopazo, Joaquin uhttp://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_2/W34002142nas a2200253 4500008004100000245010200041210006900143300001100212490000700223520138600230653001501616653002401631100002401655700001801679700001601697700001401713700001501727700001601742700002001758700001501778700001701793700001501810856006301825 2008 eng d00aBabelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments0 aBabelomics advanced functional profiling of transcriptomics prot aW341-60 v363 aWe present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the ’de novo’ functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org.
10ababelomics10afuntional profiling1 aAl-Shahrour, Fatima1 aCarbonell, J.1 aMinguez, P.1 aGoetz, S.1 aConesa, A.1 aTarraga, J.1 aMedina, Ignacio1 aAlloza, E.1 aMontaner, D.1 aDopazo, J. uhttp://nar.oxfordjournals.org/content/36/suppl_2/W341.long02196nas a2200217 4500008004100000245016500041210006900206300001000275490000700285520140700292653001501699653003501714100002401749700001601773700001601789700002001805700001501825700001701840700001501857856010601872 2007 eng d00aFatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments0 aFatiGO a functional profiling tool for genomic data Integration aW91-60 v353 aThe ultimate goal of any genome-scale experiment is to provide a functional interpretation of the data, relating the available information with the hypotheses that originated the experiment. Thus, functional profiling methods have become essential in diverse scenarios such as microarray experiments, proteomics, etc. We present the FatiGO+, a web-based tool for the functional profiling of genome-scale experiments, specially oriented to the interpretation of microarray experiments. In addition to different functional annotations (gene ontology, KEGG pathways, Interpro motifs, Swissprot keywords and text-mining based bioentities related to diseases and chemical compounds) FatiGO+ includes, as a novelty, regulatory and structural information. The regulatory information used includes predictions of targets for distinct regulatory elements (obtained from the Transfac and CisRed databases). Additionally FatiGO+ uses predictions of target motifs of miRNA to infer which of these can be activated or deactivated in the sample of genes studied. Finally, properties of gene products related to their relative location and connections in the interactome have also been used. Also, enrichment of any of these functional terms can be directly analysed on chromosomal coordinates. FatiGO+ can be found at: http://www.fatigoplus.org and within the Babelomics environment http://www.babelomics.org.
10ababelomics10afunctional enrichment analysys1 aAl-Shahrour, Fatima1 aMinguez, P.1 aTarraga, J.1 aMedina, Ignacio1 aAlloza, E.1 aMontaner, D.1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1747850402367nas a2200229 4500008004100000245007200041210006900113300000800182490000600190520145600196653010501652653001501757653013601772100002401908700001501932700001501947700002101962700001601983700001701999700001502016856010602031 2007 eng d00aFrom genes to functional classes in the study of biological systems0 aFrom genes to functional classes in the study of biological syst a1140 v83 aBACKGROUND: With the popularization of high-throughput techniques, the need for procedures that help in the biological interpretation of results has increased enormously. Recently, new procedures inspired in systems biology criteria have started to be developed. RESULTS: Here we present FatiScan, a web-based program which implements a threshold-independent test for the functional interpretation of large-scale experiments that does not depend on the pre-selection of genes based on the multiple application of independent tests to each gene. The test implemented aims to directly test the behaviour of blocks of functionally related genes, instead of focusing on single genes. In addition, the test does not depend on the type of the data used for obtaining significance values, and consequently different types of biologically informative terms (gene ontology, pathways, functional motifs, transcription factor binding sites or regulatory sites from CisRed) can be applied to different classes of genome-scale studies. We exemplify its application in microarray gene expression, evolution and interactomics. CONCLUSION: Methods for gene set enrichment which, in addition, are independent from the original data and experimental design constitute a promising alternative for the functional profiling of genome-scale experiments. A web server that performs the test described and other similar ones can be found at: http://www.babelomics.org.
10aAlgorithms Chromosome Mapping/*methods Computer Simulation Gene Expression Profiling/methods *Models10ababelomics10aBiological Multigene Family/*physiology Signal Transduction/*physiology *Software Systems Biology/*methods *User-Computer Interface1 aAl-Shahrour, Fatima1 aArbiza, L.1 aDopazo, H.1 aHuerta-Cepas, J.1 aMinguez, P.1 aMontaner, D.1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1740759601696nas a2200193 4500008004100000245009300041210006900134300001000203490000600213520105200219653001501271100001401286700001701300700002401317700001601341700002401357700001501381856010601396 2007 eng d00aFunctional profiling and gene expression analysis of chromosomal copy number alterations0 aFunctional profiling and gene expression analysis of chromosomal a432-50 v13 aContrarily to the traditional view in which only one or a few key genes were supposed to be the causative factors of diseases, we discuss the importance of considering groups of functionally related genes in the study of pathologies characterised by chromosomal copy number alterations. Recent observations have reported the existence of regions in higher eukaryotic chromosomes (including humans) containing genes of related function that show a high degree of coregulation. Copy number alterations will consequently affect to clusters of functionally related genes, which will be the final causative agents of the diseased phenotype, in many cases. Therefore, we propose that the functional profiling of the regions affected by copy number alterations must be an important aspect to take into account in the understanding of this type of pathologies. To illustrate this, we present an integrated study of DNA copy number variations, gene expression along with the functional profiling of chromosomal regions in a case of multiple myeloma.
10ababelomics1 aConde, L.1 aMontaner, D.1 aBurguet-Castell, J.1 aTarraga, J.1 aAl-Shahrour, Fatima1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1759793501608nas a2200193 4500008004100000245008900041210006900130300001100199490000700210520077100217653003900988653001501027653019401042100001601236700002401252700001701276700001501293856010601308 2007 eng d00aFunctional profiling of microarray experiments using text-mining derived bioentities0 aFunctional profiling of microarray experiments using textmining a3098-90 v233 aMOTIVATION: The increasing use of microarray technologies brought about a parallel demand in methods for the functional interpretation of the results. Beyond the conventional functional annotations for genes, such as gene ontology, pathways, etc. other sources of information are still to be exploited. Text-mining methods allow extracting informative terms (bioentities) with different functional, chemical, clinical, etc. meanings, that can be associated to genes. We show how to use these associations within an appropriate statistical framework and how to apply them through easy-to-use, web-based environments to the functional interpretation of microarray experiments. Functional enrichment and gene set enrichment tests using bioentities are presented.
10aArtificial Intelligence *Databases10ababelomics10aProtein Gene Expression Profiling/*methods Information Storage and Retrieval/*methods *Natural Language Processing Proteins/*classification/*metabolism Research/*methods Systems Integration1 aMinguez, P.1 aAl-Shahrour, Fatima1 aMontaner, D.1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1785541500560nas a2200169 4500008004100000022001800041245005100059210005100110260005300161300001200214653001500226100001500241700001600256700001400272700001700286856008700303 2007 eng d a0-4153-7853-200aMicroarray Technology in Agricultural Research0 aMicroarray Technology in Agricultural Research bF. Falciani. Publisher: Taylor and Francis Group a173-20910ababelomics1 aConesa, A.1 aForment, J.1 aGadea, J.1 avan Dijk, J. uhttps://www.clinbioinfosspa.es/content/microarray-technology-agricultural-research01384nas a2200193 4500008004100000245007300041210006900114300001000183490000700193520078700200653001500987653001001002653001501012100002001027700001701047700001601064700001501080856009501095 2007 eng d00aProphet, a web-based tool for class prediction using microarray data0 aProphet a webbased tool for class prediction using microarray da a390-10 v233 aSample classification and class prediction is the aim of many gene expression studies. We present a web-based application, Prophet, which builds prediction rules and allows using them for further sample classification. Prophet automatically chooses the best classifier, along with the optimal selection of genes, using a strategy that renders unbiased cross-validated errors. Prophet is linked to different microarray data analysis modules, and includes a unique feature: the possibility of performing the functional interpretation of the molecular signature found. Availability: Prophet can be found at the URL http://prophet.bioinfo.cipf.es/ or within the GEPAS package at http://www.gepas.org/ Supplementary information: http://gepas.bioinfo.cipf.es/tutorial/prophet.html.
10ababelomics10agepas10apredictors1 aMedina, Ignacio1 aMontaner, D.1 aTarraga, J.1 aDopazo, J. uhttp://bioinformatics.oxfordjournals.org/cgi/content/full/23/3/390?view=long&pmid=1713858701445nas a2200253 4500008004100000245010300041210006900144300001100213490000700224520068700231653001500918653002500933100002400958700001600982700001600998700001701014700001501031700002301046700001401069700001701083700001301100700001501113856006301128 2006 eng d00aBABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments0 aBABELOMICS a systems biology perspective in the functional annot aW472-60 v343 aWe present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at http://www.babelomics.org.
10ababelomics10afunctional profiling1 aAl-Shahrour, Fatima1 aMinguez, P.1 aTarraga, J.1 aMontaner, D.1 aAlloza, E.1 aVaquerizas, J., M.1 aConde, L.1 aBlaschke, C.1 aVera, J.1 aDopazo, J. uhttp://nar.oxfordjournals.org/content/34/suppl_2/W472.long02376nas 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 aThe 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=1682313801588nas a2200157 4500008004100000245005600041210005600097300001200153490000700165520107100172653001501243653002201258653002901280100001501309856010601324 2006 eng d00aFunctional interpretation of microarray experiments0 aFunctional interpretation of microarray experiments a398-4100 v103 aOver the past few years, due to the popularisation of high-throughput methodologies such as DNA microarrays, the possibility of obtaining experimental data has increased significantly. Nevertheless, the interpretation of the results, which involves translating these data into useful biological knowledge, still remains a challenge. The methods and strategies used for this interpretation are in continuous evolution and new proposals are constantly arising. Initially, a two-step approach was used in which genes of interest were initially selected, based on thresholds that consider only experimental values, and then in a second, independent step the enrichment of these genes in biologically relevant terms, was analysed. For different reasons, these methods are relatively poor in terms of performance and a new generation of procedures, which draw inspiration from systems biology criteria, are currently under development. Such procedures, aim to directly test the behaviour of blocks of functionally related genes, instead of focusing on single genes.
10ababelomics10aDiabetes Mellitus10amicroarray data analysis1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1706951602404nas a2200157 4500008004100000245009100041210006900132300001000201490000700211520184000218653001502058100001602073700002402089700001502113856011802128 2006 eng d00aA function-centric approach to the biological interpretation of microarray time-series0 afunctioncentric approach to the biological interpretation of mic a57-660 v173 aThe interpretation of microarray experiments is commonly addressed by means a two-step approach in which the relevant genes are firstly selected uniquely on the basis of their experimental values (ignoring their coordinate behaviors) and in a second step their functional properties are studied to hypothesize about the biological roles they are fulfilling in the cell. Recently, different methods (e.g. GSEA or FatiScan) have been proposed to study the coordinate behavior of blocks of functionally-related genes. These methods study the distribution of functional information across lists of genes ranked according their different experimental values in a static situation, such as the comparison between two classes (e.g. healthy controls versus diseased cases). Nevertheless there is no an equivalent way of studying a dynamic situation from a functional point of view. We present a method for the functional analysis of microarrays series in which the experiments display autocorrelation between successive points (e.g. time series, dose-response experiments, etc.) The method allows to recover the dynamics of the molecular roles fulfilled by the genes along the series which provides a novel approach to functional interpretation of such experiments. The method finds blocks of functionally-related genes which are significantly and coordinately over-expressed at different points of the series. This method draws inspiration from systems biology given that the analysis does not focus on individual properties of genes but on collective behaving blocks of functionally-related genes. The FatiScan algorithm used in the method proposed is available at: http://fatiscan.bioinfo.cipf.es, or within the Babelomics suite: http://www.babelomics.org. Additional material is available at: http://bioinfo.cipf.es/data/plasmodium.
10ababelomics1 aMinguez, P.1 aAl-Shahrour, Fatima1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/function-centric-approach-biological-interpretation-microarray-time-series01646nas a2200217 4500008004100000245007200041210006900113300001000182490000800192520083200200653001501032653002101047653007301068653002601141653004201167653005901209100001501268700002401283700001501307856010601322 2006 eng d00aOntology-driven approaches to analyzing data in functional genomics0 aOntologydriven approaches to analyzing data in functional genomi a67-860 v3163 aOntologies are fundamental knowledge representations that provide not only standards for annotating and indexing biological information, but also the basis for implementing functional classification and interpretation models. This chapter discusses the application of gene ontology (GO) for predictive tasks in functional genomics. It focuses on the problem of analyzing functional patterns associated with gene products. This chapter is divided into two main parts. The first part overviews GO and its applications for the development of functional classification models. The second part presents two methods for the characterization of genomic information using GO. It discusses methods for measuring functional similarity of gene products, and a tool for supporting gene expression clustering analysis and validation.
10ababelomics10aCluster Analysis10aCluster Analysis Computational Biology/*methods *Data Interpretation10aComputational Biology10aStatistical Gene Expression Profiling10aStatistical Gene Expression Profiling *Genomics Humans1 aAzuaje, F.1 aAl-Shahrour, Fatima1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1667140102090nas a2200193 4500008004100000245012600041210006900167300001100236490000700247520144700254653001501701653002501716100002401741700001601765700002301781700001401804700001501818856006301833 2005 eng d00aBABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments0 aBABELOMICS a suite of web tools for functional annotation and an aW460-40 v333 aWe present Babelomics, a complete suite of web tools for the functional analysis of groups of genes in high-throughput experiments, which includes the use of information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence in tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool, respectively. Additionally, another module, FatiScan, provides a new procedure that integrates biological information in combination with experimental results in order to find groups of genes with modest but coordinate significant differential behaviour. FatiScan is highly sensitive and is capable of finding significant asymmetries in the distribution of genes of common function across a list of ordered genes even if these asymmetries were not extreme. The strong multiple-testing nature of the contrasts made by the tools is taken into account. All the tools are integrated in the gene expression analysis package GEPAS. Babelomics is the natural evolution of our tool FatiGO (which analysed almost 22,000 experiments during the last year) to include more sources on information and new modes of using it. Babelomics can be found at http://www.babelomics.org.
10ababelomics10afunctional profiling1 aAl-Shahrour, Fatima1 aMinguez, P.1 aVaquerizas, J., M.1 aConde, L.1 aDopazo, J. uhttp://nar.oxfordjournals.org/content/33/suppl_2/W460.long01401nas 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 aSUMMARY: 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=1608147400468nas a2200121 4500008004100000245006300041210006300104260003500167653001500202100001500217700001500232856009900247 2005 eng d00aData analysis and visualisation in genomics and proteomics0 aData analysis and visualisation in genomics and proteomics bWiley, F. Azuaje and J. Dopazo10ababelomics1 aAzuaje, F.1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/data-analysis-and-visualisation-genomics-and-proteomics02842nas a2200205 4500008004100000245013300041210006900174300001200243490000700255520183200262653001502094653013902109653003602248653010202284653008402386100002402470700002102494700001502515856010602530 2005 eng d00aDiscovering molecular functions significantly related to phenotypes by combining gene expression data and biological information0 aDiscovering molecular functions significantly related to phenoty a2988-930 v213 aMOTIVATION: The analysis of genome-scale data from different high throughput techniques can be used to obtain lists of genes ordered according to their different behaviours under distinct experimental conditions corresponding to different phenotypes (e.g. differential gene expression between diseased samples and controls, different response to a drug, etc.). The order in which the genes appear in the list is a consequence of the biological roles that the genes play within the cell, which account, at molecular scale, for the macroscopic differences observed between the phenotypes studied. Typically, two steps are followed for understanding the biological processes that differentiate phenotypes at molecular level: first, genes with significant differential expression are selected on the basis of their experimental values and subsequently, the functional properties of these genes are analysed. Instead, we present a simple procedure which combines experimental measurements with available biological information in a way that genes are simultaneously tested in groups related by common functional properties. The method proposed constitutes a very sensitive tool for selecting genes with significant differential behaviour in the experimental conditions tested. RESULTS: We propose the use of a method to scan ordered lists of genes. The method allows the understanding of the biological processes operating at molecular level behind the macroscopic experiment from which the list was generated. This procedure can be useful in situations where it is not possible to obtain statistically significant differences based on the experimental measurements (e.g. low prevalence diseases, etc.). Two examples demonstrate its application in two microarray experiments and the type of information that can be extracted.
10ababelomics10aBiological Neoplasm Proteins/genetics/*metabolism Phenotype Software Structure-Activity Relationship Systems Integration Tumor Markers10aBiological/genetics/*metabolism10aBreast Neoplasms/genetics/*metabolism Computer Simulation *Database Management Systems *Databases10aProtein Documentation/methods Gene Expression Profiling/*methods Humans *Models1 aAl-Shahrour, Fatima1 aDiaz-Uriarte, R.1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1584070201450nas a2200193 4500008004100000245010400041210006900145300001100214490000700225520063300232653005000865653001500915653002700930653016800957100002401125700002101149700001501170856007101185 2004 eng d00aFatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes0 aFatiGO a web tool for finding significant associations of Gene O a578-800 v203 aWe present a simple but powerful procedure to extract Gene Ontology (GO) terms that are significantly over- or under-represented in sets of genes within the context of a genome-scale experiment (DNA microarray, proteomics, etc.). Said procedure has been implemented as a web application, FatiGO, allowing for easy and interactive querying. FatiGO, which takes the multiple-testing nature of statistical contrast into account, currently includes GO associations for diverse organisms (human, mouse, fly, worm and yeast) and the TrEMBL/Swissprot GOAnnotations@EBI correspondences from the European Bioinformatics Institute.
10a*Algorithms Artificial Intelligence Databases10ababelomics10aDNA/*methods *Software10aGenetic Gene Expression Profiling/*methods *Hypermedia Information Storage and Retrieval/*methods *Internet *Phylogeny Sequence Alignment/methods Sequence Analysis1 aAl-Shahrour, Fatima1 aDiaz-Uriarte, R.1 aDopazo, J. uhttp://bioinformatics.oxfordjournals.org/content/20/4/578.abstract00720nas a2200181 4500008004100000245013000041210006900171260003000240300001000270653001500280100002400295700001600319700001500335700001600350700002100366700001500387856013600402 2003 eng d00aUsing Gene Ontology on genome-scale studies to find significant associations of biologically relevant terms to group of genes0 aUsing Gene Ontology on genomescale studies to find significant a aNew York, USAbIEEE Press a43-5210ababelomics1 aAl-Shahrour, Fatima1 aHerrero, J.1 aMateos, A.1 aSantoyo, J.1 aDíaz-Uriarte, R1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/using-gene-ontology-genome-scale-studies-find-significant-associations-biologically-relevant