Jari Häkkinen

GOBO: Gene Expression-Based Outcome for Breast Cancer Online.

Microarray-based gene expression analysis holds promise of improving prognostication and treatment decisions for breast cancer patients. However, the heterogeneity of breast cancer emphasizes the need for validation of prognostic gene signatures in larger sample sets stratified into relevant subgroups. Here, we describe a multifunctional user-friendly online tool, GOBO (http://co.bmc.lu.se/gobo), allowing a range of different analyses to be performed in an 1881-sample breast tumor data set, and a 51-sample breast cancer cell line set, both generated on Affymetrix U133A microarrays. GOBO supports a wide range of applications including: 1) rapid assessment of gene expression levels in subgroups of breast tumors and cell lines, 2) identification of co-expressed genes for creation of potential metagenes, 3) association with outcome for gene expression levels of single genes, sets of genes, or gene signatures in multiple subgroups of the 1881-sample breast cancer data set. The design and implementation of GOBO facilitate easy incorporation of additional query functions and applications, as well as additional data sets irrespective of tumor type and array platform.

The Proteios Software Environment: an extensible multiuser platform for management and analysis of proteomics data

Proteome analysis involves many steps that generate large quantities of data in different formats. This creates a need for automatic data merging and extraction of important features from data. Furthermore, metadata need to be collected and reported to enable critical evaluation of results. Many data analysis tools are developed locally in research laboratories and are nontrivial to adapt for other laboratories, preventing optimal exploitation of generated data. The proteomics field would benefit from user-friendly analysis and data management platforms in which method developers can make their analysis tools available for the community. Here, we describe the Proteios Software Environment (ProSE) that is built around a Web-based local data repository for proteomics experiments. The application features sample tracking, project sharing between multiple users, and automated data merging and analysis. ProSE has built-in support for several quantitative proteomics workflows, and integrates searching in several search engines, automated combination of the search results with predetermined false discovery rates, annotation of proteins and submission of results to public repositories. ProSE also provides a programming interface to enable local extensions, as well as database access using Web services. ProSE provides an analysis platform for proteomics research and is targeted for multiuser projects with needs to share data, sample tracking, and analysis result. ProSE is open source software available at http://www.proteios.org .

BASE--2nd generation software for microarray data management and analysis.

BackgroundMicroarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2.ResultsThe new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE.ConclusionBASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.

PROTEIOS: an open source proteomics initiative

SUMMARY PROTEIOS is an initiative for the development of a comprehensive open source system for storage, organization, analysis and annotation of proteomics experiments. The PROTEIOS platform is based on commonly acknowledged principles for proteomics data publishing. AVAILABILITY http://www.proteios.org

ACID: a database for microarray clone information

SUMMARY Array Close Information Database is an online database for information about microarray cDNA clones. For each clone, the database contents include assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly. AVAILABILITY http://bioinfo.thep.lu.se/acid.html

Lambda-polarization in e+e--annihilation at the Z0-pole

Strange quarks produced in e+e--annihilation at the Z0-pole are very strongly polarized. To study to which extent this polarization is transferred to the observable hadrons would give interesting information on the hadronization mechanism. Γ-particles produced with relatively large x-values are expected to frequently contain an originally produced s-quark. We estimate that Γ-particles with x>0.3 should have a longitudinal polarization of about 30%.

Improving missing value imputation of microarray data by using spot quality weights

BackgroundMicroarray technology has become popular for gene expression profiling, and many analysis tools have been developed for data interpretation. Most of these tools require complete data, but measurement values are often missing A way to overcome the problem of incomplete data is to impute the missing data before analysis. Many imputation methods have been suggested, some naïve and other more sophisticated taking into account correlation in data. However, these methods are binary in the sense that each spot is considered either missing or present. Hence, they are depending on a cutoff separating poor spots from good spots. We suggest a different approach in which a continuous spot quality weight is built into the imputation methods, allowing for smooth imputations of all spots to larger or lesser degree.ResultsWe assessed several imputation methods on three data sets containing replicate measurements, and found that weighted methods performed better than non-weighted methods. Of the compared methods, best performance and robustness were achieved with the weighted nearest neighbours method (WeNNI), in which both spot quality and correlations between genes were included in the imputation.ConclusionIncluding a measure of spot quality improves the accuracy of the missing value imputation. WeNNI, the proposed method is more accurate and less sensitive to parameters than the widely used kNNimpute and LSimpute algorithms.

Colour Connections in e+e- annihilation

We have a very limited knowledge about how the confinement mechanism works in processes like

Molecular microheterogeneity of prostate specific antigen in seminal fluid by mass spectrometry.

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Colour interference and confinement effects in W-pair production

, when there are identical colour charges. In this case the partons can be colour connected by a string or a cluster chain in several different ways. We do not know if in such a situation Nature chooses a particular configuration at random, or if some configuration is dynamically favoured. Also in the perturbative parton cascade we have no well founded recipe for describing the interference effects, which correspond to non planar diagrams and are caused by identical colour charges. We have studied two different models, and are in particular interested in the possibility that a colour singlet gluon system hadronizes isolated from the remainder of the state. Using double tagged events with heavy