sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters

<p>Abstract</p> <p>Background</p> <p>Microarray is a powerful technology enabling to monitor tens of thousands of genes in a single experiment. Most microarrays are now using oligo-sets. The design of the oligo-nucleotides is time consuming and error prone. Genome wide microarray oligo-sets are designed using as large a set of transcripts as possible in order to monitor as many genes as possible. Depending on the genome sequencing state and on the assembly state the knowledge of the existing transcripts can be very different. This knowledge evolves with the different genome builds and gene builds. Once the design is done the microarrays are often used for several years. The biologists working in EADGENE expressed the need of up-to-dated annotation files for the oligo-sets they share including information about the orthologous genes of model species, the Gene Ontology, the corresponding pathways and the chromosomal location.</p> <p>Results</p> <p>The results of SigReannot on a chicken micro-array used in the EADGENE project compared to the initial annotations show that 23% of the oligo-nucleotide gene annotations were not confirmed, 2% were modified and 1% were added. The interest of this up-to-date annotation procedure is demonstrated through the analysis of real data previously published.</p> <p>Conclusion</p> <p>SigReannot uses the oligo-nucleotide design procedure criteria to validate the probe-gene link and the Ensembl transcripts as reference for annotation. It therefore produces a high quality annotation based on reference gene sets.</p

Transcriptome profiling of the feeding-to-fasting transition in chicken liver

<p>Abstract</p> <p>Background</p> <p>Starvation triggers a complex array of adaptative metabolic responses including energy-metabolic responses, a process which must imply tissue specific alterations in gene expression and in which the liver plays a central role. The present study aimed to describe the evolution of global gene expression profiles in liver of 4-week-old male chickens during a 48 h fasting period using a chicken 20 K oligoarray.</p> <p>Results</p> <p>A large number of genes were modulated by fasting (3532 genes with a pvalue corrected by Benjamini-Hochberg < 0.01); 2062 showed an amplitude of variation higher than +/- 40% among those, 1162 presented an human ortholog, allowing to collect functional information. Notably more genes were down-regulated than up-regulated, whatever the duration of fasting (16 h or 48 h). The number of genes differentially expressed after 48 h of fasting was 3.5-fold higher than after 16 h of fasting. Four clusters of co-expressed genes were identified by a hierarchical cluster analysis. Gene Ontology, KEGG and Ingenuity databases were then used to identify the metabolic processes associated to each cluster. After 16 h of fasting, genes involved in ketogenesis, gluconeogenesis and mitochondrial or peroxisomal fatty acid beta-oxidation, were up-regulated (cluster-1) whereas genes involved in fatty acid and cholesterol synthesis were down-regulated (cluster-2). For all genes tested, the microarray data was confirmed by quantitative RT-PCR. Most genes were altered by fasting as already reported in mammals. A notable exception was the <it>HMG-CoA synthase 1 </it>gene, which was up-regulated following 16 and 48 h of fasting while the other genes involved in cholesterol metabolism were down-regulated as reported in mammalian studies. We further focused on genes not represented on the microarray and candidates for the regulation of the target genes belonging to cluster-1 and -2 and involved in lipid metabolism. Data are provided concerning PPARa, SREBP1, SREBP2, NR1H3 transcription factors and two desaturases (FADS1, FADS2).</p> <p>Conclusion</p> <p>This study evidences numerous genes altered by starvation in chickens and suggests a global repression of cellular activity in response to this stressor. The central role of lipid and acetyl-CoA metabolisms and its regulation at transcriptional level are confirmed in chicken liver in response to short-term fasting. Interesting expression modulations were observed for <it>NR1H3, FADS1 </it>and <it>FADS2 </it>genes. Further studies are needed to precise their role in the complex regulatory network controlling lipid metabolism.</p

Oocyte-somatic cells interactions, lessons from evolution

BACKGROUND: Despite the known importance of somatic cells for oocyte developmental competence acquisition, the overall mechanisms underlying the acquisition of full developmental competence are far from being understood, especially in non-mammalian species. The present work aimed at identifying key molecular signals from somatic origin that would be shared by vertebrates. RESULTS: Using a parallel transcriptomic analysis in 4 vertebrate species - a teleost fish, an amphibian, and two mammals - at similar key steps of developmental competence acquisition, we identified a large number of species-specific differentially expressed genes and a surprisingly high number of orthologous genes exhibiting similar expression profiles in the 3 tetrapods and in the 4 vertebrates. Among the evolutionary conserved players participating in developmental competence acquisition are genes involved in key processes such as cellular energy metabolism, cell-to-cell communications, and meiosis control. In addition, we report many novel molecular actors from somatic origin that have never been studied in the vertebrate ovary. Interestingly, a significant number of these new players actively participate in Drosophila oogenesis. CONCLUSIONS: Our study provides a comprehensive overview of evolutionary-conserved mechanisms from somatic origin participating in oocyte developmental competence acquisition in 4 vertebrates. Together our results indicate that despite major differences in ovarian follicular structure, some of the key players from somatic origin involved in oocyte developmental competence acquisition would be shared, not only by vertebrates, but also by metazoans. The conservation of these mechanisms during vertebrate evolution further emphasizes the important contribution of the somatic compartment to oocyte quality and paves the way for future investigations aiming at better understanding what makes a good egg

Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase

Background: Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description: In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.htm l. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion: A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism

QBIOS: driving toward a trusted distributed bioinformatics service infrastructure

International audienceWith the proliferation of bioinformatics web services, innovative on-tology based frameworks have been developed to allow an efficient service discovery process, but they do not provide semantic annota-tions regarding services availability and reliability. To fill this gap, and because the quality of service is a major factor that limits the success of promising service oriented architecture in bioinformatics, we created QBIOS, an automatic test engine dedicated to bioinfor-matics services. QBIOS allows service test case creation, scheduled execution and distributed monitoring. It provides reliable quality of service indicators that can be used in workflow management sys-tems and shared to build community based service repositories and trustable searching engines

Concevoir et partager des workflows d’analyse de données : application aux traitements intensifs en bioinformatique

As part of an Open Science initiative, we are particularly interested in the scientific Workflow Management Systems (WfMS) and their applications for intensive data analysis in bioinformatics. We start from the assumption that WfMS can evolve to become efficient hubs able to speed up the development and the dissemination of innovative analysis methods. These software platforms could rally and unite not only the current stakeholders, who are service consumers, but also the service producers, around a disciplinary theme. We therefore consider that these environments must be both adapted to the practices of the scientists who are method designers and also enhanced with increased productivity during design and treatment. These constraints lead us to study the rapid capture of workflows, the simplification of technical tasks integration, like parallelisation and the deployment customization. First, we define an expressive graphic worfklow language, adapted to the quick capture of workflows. This is interpreted by a workflow engine based on a new model of computation with high performances obtained by the use of multiple levels of parallelism. Then, we present a Model-Driven design approach that facilitates the data parallelism generation and the production of suitable implementations for different execution contexts. We describe in particular the integration of a components and platforms meta-model used to automate the configuration of workflows’ dependencies. Finally, in the case of the cloud model Container as a Service (CaaS), we develop a workflow specification intrinsically re-executable and readily disseminatable. The adoption of this kind of model could lead to an acceleration of exchanges and a better availability of data analysis workflows.Dans le cadre d'une démarche d'Open science, nous nous intéressons aux systèmes de gestion de workflows (WfMS) scientifiques et à leurs applications pour l'analyse de données intensive en bioinformatique. Nous partons de l'hypothèse que les WfMS peuvent évoluer pour devenir des plates-formes pivots capables d'accélérer la mise au point et la diffusion de méthodes d'analyses innovantes. Elles pourraient capter et fédérer autour d'une thématique disciplinaire non seulement le public actuel des consommateurs de services mais aussi celui des producteurs de services. Pour cela, nous considérons que ces environnements doivent à la fois être adaptés aux pratiques des scientifiques concepteurs de méthodes et fournir un gain de productivité durant la conception et le traitement. Ces contraintes nous amènent à étudier la capture rapide des workflows, la simplification de l'intégration des tâches techniques, comme le parallélisme nécessaire au haut-débit, et la personnalisation du déploiement. Tout d'abord, nous avons défini un langage graphique DataFlow expressif, adapté à la capture rapide des workflows. Celui-ci est interprétable par un moteur de workflows basé sur un nouveau modèle de calcul doté de performances élevées, obtenues par l'exploitation des multiples niveaux de parallélisme. Nous présentons ensuite une approche de conception orientée modèle qui facilite la génération du parallélisme de données et la production d'implémentations adaptées à différents contextes d'exécution. Nous décrivons notamment l'intégration d'un métamodèle des composants et des plates-formes, employé pour automatiser la configuration des dépendances des workflows. Enfin, dans le cas du modèle Container as a Service (CaaS), nous avons élaboré une spécification de workflows intrinsèquement diffusable et ré-exécutable. L'adoption de ce type de modèle pourrait déboucher sur une accélération des échanges et de la mise à disposition des chaînes de traitements d'analyse de données

A framework for building reliable distributed bioinformatics service repositories

International audienceThe reliability is a major factor that limits the success of promising service oriented architecture in bioinformatics. To evaluate services reliability and availability and create indicators of quality of service, we have defined an XML format designed to exchange service status reports. We demonstrate the interest of sharing status reports between service consumers and producers by providing two example applications, a workflow management system plugin and a web report generator. Furthermore, we describe the framework that we use to distribute quality of service management features, QBIOS. QBIOS enables service test case creation, scheduled execution and monitoring. We illustrate the use of our open test strategy at the level of a group of scientific partners sharing bioinformatics services

Design and share data analysis workflows : application to bioinformatics intensive treatments

Dans le cadre d'une démarche d'Open science, nous nous intéressons aux systèmes de gestion de workflows (WfMS) scientifiques et à leurs applications pour l'analyse de données intensive en bioinformatique. Nous partons de l'hypothèse que les WfMS peuvent évoluer pour devenir des plates-formes pivots capables d'accélérer la mise au point et la diffusion de méthodes d'analyses innovantes. Elles pourraient capter et fédérer autour d'une thématique disciplinaire non seulement le public actuel des consommateurs de services mais aussi celui des producteurs de services. Pour cela, nous considérons que ces environnements doivent à la fois être adaptés aux pratiques des scientifiques concepteurs de méthodes et fournir un gain de productivité durant la conception et le traitement. Ces contraintes nous amènent à étudier la capture rapide des workflows, la simplification de l'intégration des tâches techniques, comme le parallélisme nécessaire au haut-débit, et la personnalisation du déploiement. Tout d'abord, nous avons défini un langage graphique DataFlow expressif, adapté à la capture rapide des workflows. Celui-ci est interprétable par un moteur de workflows basé sur un nouveau modèle de calcul doté de performances élevées, obtenues par l'exploitation des multiples niveaux de parallélisme. Nous présentons ensuite une approche de conception orientée modèle qui facilite la génération du parallélisme de données et la production d'implémentations adaptées à différents contextes d'exécution. Nous décrivons notamment l'intégration d'un métamodèle des composants et des plates-formes, employé pour automatiser la configuration des dépendances des workflows. Enfin, dans le cas du modèle Container as a Service (CaaS), nous avons élaboré une spécification de workflows intrinsèquement diffusable et ré-exécutable. L'adoption de ce type de modèle pourrait déboucher sur une accélération des échanges et de la mise à disposition des chaînes de traitements d'analyse de données.As part of an Open Science initiative, we are particularly interested in the scientific Workflow Management Systems (WfMS) and their applications for intensive data analysis in bioinformatics. We start from the assumption that WfMS can evolve to become efficient hubs able to speed up the development and the dissemination of innovative analysis methods. These software platforms could rally and unite not only the current stakeholders, who are service consumers, but also the service producers, around a disciplinary theme. We therefore consider that these environments must be both adapted to the practices of the scientists who are method designers and also enhanced with increased productivity during design and treatment. These constraints lead us to study the rapid capture of workflows, the simplification of technical tasks integration, like parallelisation and the deployment customization. First, we define an expressive graphic worfklow language, adapted to the quick capture of workflows. This is interpreted by a workflow engine based on a new model of computation with high performances obtained by the use of multiple levels of parallelism. Then, we present a Model-Driven design approach that facilitates the data parallelism generation and the production of suitable implementations for different execution contexts. We describe in particular the integration of a components and platforms meta-model used to automate the configuration of workflows’ dependencies. Finally, in the case of the cloud model Container as a Service (CaaS), we develop a workflow specification intrinsically re-executable and readily disseminatable. The adoption of this kind of model could lead to an acceleration of exchanges and a better availability of data analysis workflows

Concevoir et partager des workflows d’analyse de données : application aux traitements intensifs en bioinformatique

As part of an Open Science initiative, we are particularly interested in the scientific Workflow Management Systems (WfMS) and their applications for intensive data analysis in bioinformatics. We start from the assumption that WfMS can evolve to become efficient hubs able to speed up the development and the dissemination of innovative analysis methods. These software platforms could rally and unite not only the current stakeholders, who are service consumers, but also the service producers, around a disciplinary theme. We therefore consider that these environments must be both adapted to the practices of the scientists who are method designers and also enhanced with increased productivity during design and treatment. These constraints lead us to study the rapid capture of workflows, the simplification of technical tasks integration, like parallelisation and the deployment customization. First, we define an expressive graphic worfklow language, adapted to the quick capture of workflows. This is interpreted by a workflow engine based on a new model of computation with high performances obtained by the use of multiple levels of parallelism. Then, we present a Model-Driven design approach that facilitates the data parallelism generation and the production of suitable implementations for different execution contexts. We describe in particular the integration of a components and platforms meta-model used to automate the configuration of workflows’ dependencies. Finally, in the case of the cloud model Container as a Service (CaaS), we develop a workflow specification intrinsically re-executable and readily disseminatable. The adoption of this kind of model could lead to an acceleration of exchanges and a better availability of data analysis workflows.Dans le cadre d'une démarche d'Open science, nous nous intéressons aux systèmes de gestion de workflows (WfMS) scientifiques et à leurs applications pour l'analyse de données intensive en bioinformatique. Nous partons de l'hypothèse que les WfMS peuvent évoluer pour devenir des plates-formes pivots capables d'accélérer la mise au point et la diffusion de méthodes d'analyses innovantes. Elles pourraient capter et fédérer autour d'une thématique disciplinaire non seulement le public actuel des consommateurs de services mais aussi celui des producteurs de services. Pour cela, nous considérons que ces environnements doivent à la fois être adaptés aux pratiques des scientifiques concepteurs de méthodes et fournir un gain de productivité durant la conception et le traitement. Ces contraintes nous amènent à étudier la capture rapide des workflows, la simplification de l'intégration des tâches techniques, comme le parallélisme nécessaire au haut-débit, et la personnalisation du déploiement. Tout d'abord, nous avons défini un langage graphique DataFlow expressif, adapté à la capture rapide des workflows. Celui-ci est interprétable par un moteur de workflows basé sur un nouveau modèle de calcul doté de performances élevées, obtenues par l'exploitation des multiples niveaux de parallélisme. Nous présentons ensuite une approche de conception orientée modèle qui facilite la génération du parallélisme de données et la production d'implémentations adaptées à différents contextes d'exécution. Nous décrivons notamment l'intégration d'un métamodèle des composants et des plates-formes, employé pour automatiser la configuration des dépendances des workflows. Enfin, dans le cas du modèle Container as a Service (CaaS), nous avons élaboré une spécification de workflows intrinsèquement diffusable et ré-exécutable. L'adoption de ce type de modèle pourrait déboucher sur une accélération des échanges et de la mise à disposition des chaînes de traitements d'analyse de données

GEO EXPORTER : a tools to automate publishing of microarray data to Gene Expression Omnibus

International audiencecurrent solutions do not allow automatic publication of microarray experiment results from a microarray data management system to one of the public repositories (Gene Expression Omnibus, ArrayExpress). The end-user is generally involved in various steps of the process which results in low productivity. We have developed a software which allows validating, extraction and automatic publication of microarray data stored in BASE (BioArray Software Environment), a wildly used open source microarray data management system, to Gene Expression Omnibus a reference microarray data repository. The code written in PHP is especially modularized to allow a quick adaptation to any microarray data management system which could be access by SQL