CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis

CARMAweb (Comprehensive R-based Microarray Analysis web service) is a web application designed for the analysis of microarray data. CARMAweb performs data preprocessing (background correction, quality control and normalization), detection of differentially expressed genes, cluster analysis, dimension reduction and visualization, classification, and Gene Ontology-term analysis. This web application accepts raw data from a variety of imaging software tools for the most widely used microarray platforms: Affymetrix GeneChips, spotted two-color microarrays and Applied Biosystems (ABI) microarrays. R and packages from the Bioconductor project are used as an analytical engine in combination with the R function Sweave, which allows automatic generation of analysis reports. These report files contain all R commands used to perform the analysis and guarantee therefore a maximum transparency and reproducibility for each analysis. The web application is implemented in Java based on the latest J2EE (Java 2 Enterprise Edition) software technology. CARMAweb is freely available at

Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

BACKGROUND: Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the sequences of identified gene products has not been done and global mechanisms have not been investigated. We evaluated the extent to which molecular processes can be revealed by expression profiling and functional annotation of genes that are differentially expressed during fat cell development. RESULTS: Mouse microarrays with more than 27,000 elements were developed, and transcriptional profiles of 3T3-L1 cells (pre-adipocyte cells) were monitored during differentiation. In total, 780 differentially expressed expressed sequence tags (ESTs) were subjected to in-depth bioinformatics analyses. The analysis of 3'-untranslated region sequences from 395 ESTs showed that 71% of the differentially expressed genes could be regulated by microRNAs. A molecular atlas of fat cell development was then constructed by de novo functional annotation on a sequence segment/domain-wise basis of 659 protein sequences, and subsequent mapping onto known pathways, possible cellular roles, and subcellular localizations. Key enzymes in 27 out of 36 investigated metabolic pathways were regulated at the transcriptional level, typically at the rate-limiting steps in these pathways. Also, coexpressed genes rarely shared consensus transcription-factor binding sites, and were typically not clustered in adjacent chromosomal regions, but were instead widely dispersed throughout the genome. CONCLUSIONS: Large-scale transcription profiling in conjunction with sophisticated bioinformatics analyses can provide not only a list of novel players in a particular setting but also a global view on biological processes and molecular networks

MARS: Microarray analysis, retrieval, and storage system

BACKGROUND: Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. RESULTS: MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. CONCLUSION: We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

<p>Abstract</p> <p>Background</p> <p>The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires the use of data management platforms and computational approaches.</p> <p>Results</p> <p>We have developed the MAss SPECTRometry Analysis System (MASPECTRAS), a platform for management and analysis of proteomics LC-MS/MS data. MASPECTRAS is based on the Proteome Experimental Data Repository (PEDRo) relational database schema and follows the guidelines of the Proteomics Standards Initiative (PSI). Analysis modules include: 1) import and parsing of the results from the search engines SEQUEST, Mascot, Spectrum Mill, X! Tandem, and OMSSA; 2) peptide validation, 3) clustering of proteins based on Markov Clustering and multiple alignments; and 4) quantification using the Automated Statistical Analysis of Protein Abundance Ratios algorithm (ASAPRatio). The system provides customizable data retrieval and visualization tools, as well as export to PRoteomics IDEntifications public repository (PRIDE). MASPECTRAS is freely available at <url>http://genome.tugraz.at/maspectras</url></p> <p>Conclusion</p> <p>Given the unique features and the flexibility due to the use of standard software technology, our platform represents significant advance and could be of great interest to the proteomics community.</p

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

QUBIC, a specific and highly sensitive method for detection of protein–protein interactions, is used to identify new partners for the mitotic spindle components pericentrin and TACC3

Differential Expression of MicroRNAs in Adipose Tissue after Long-Term High-Fat Diet-Induced Obesity in Mice

Obesity is a major health concern worldwide which is associated with increased risk of chronic diseases such as metabolic syndrome, cardiovascular disease and cancer. The elucidation of the molecular mechanisms involved in adipogenesis and obesogenesis is of essential importance as it could lead to the identification of novel biomarkers and therapeutic targets for the development of anti-obesity drugs. MicroRNAs (miRNAs) have been shown to play regulatory roles in several biological processes. They have become a growing research field and consist of promising pharmaceutical targets in various fields such as cancer, metabolism, etc. The present study investigated the possible implication of miRNAs in adipose tissue during the development of obesity using as a model the C57BLJ6 mice fed a high-fat diet

Zwischenevaluierung des Programms "Beyond Europe"

Das ZSI bewertete das Programm "Beyond Europe" des Bundesministeriums für Digitalisierung und Wirtschaftsstandort (BMDW), das von der österreichischen Forschungsförderungsgesellschaft (FFG) durchgeführt wird. Das Programm ist mit seiner spezifischen Ausrichtung in der österreichischen Förderlandschaft einzigartig: Es unterstützt die Forschungs- und Innovationskooperation zwischen österreichischen Unternehmen und außereuropäischen Partnern, ist thematisch und geografisch offen, unter Bezugnahme auf die Prioritätenliste der Empfehlungen zur Beyond Europe-Strategie für die Zielländer. Bis jetzt gab es zwei Aufrufe (2015 und 2017), und insgesamt wurden 30 Projekte finanziert. Bereits bei der Konzeption des "Beyond Europe" -Programms war nach zwei Jahren eine erste Zwischenbewertung geplant. Die Bewertungsergebnisse fließen in den zukünftigen Programmierungs- und Ausschreibungsprozess ein und zielen darauf ab, die Programmziele und Anpassungen des Programms entsprechend den Bedürfnissen der Zielgruppe zu schärfen. Zu guter Letzt schlägt die Evaluierung Erfolgs- und Wirkungsindikatoren vor. Der Zwischenbericht behandelt die Logik und das Design des Programms, analysiert die Schlüsseldaten der Programmteilnahme, das Feedback der Programmteilnehmer, bespricht den Mehrwert des Programms auf der Grundlage von Erhebungs- und Fokusgruppendaten und gibt Vorschläge für mögliche Anpassungen in der Programmgestaltung. Darüber hinaus geben wir Empfehlungen zur Definition von Wirkungsindikatoren und präsentieren die Ergebnisse des internationalen Vergleichs mit ähnlich orientierten Programminterventionen in anderen europäischen Ländern

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

Body cremated. Katherine Eastman - wifehttps://stars.library.ucf.edu/cfm-ch-register-vol21/1495/thumbnail.jp