Microarray and gene expression are fundamental tools of nowadays Biology research. While standard formats and software systems have been developed to represent and publicly share information about microarray experiments, existing computational solutions give limited support to the representation of the outcomes, experimental hypotheses or conclusions about biological questions that are dealt with in gene expression analysis. We propose an OWL-based model and a Semantic Web-based approach to address the issue. We show that the formalization of microarray-related knowle...

We have developed, at the Curie Institute, a unique methodology dedicated to the identification of phagosome proteins in dendritic cells, under various experimental conditions. This methodoly incorporates a unique sample preparation procedure based on 96 well plate complex sample trypsinization, a nano-LC-based peptide separation coupled to MSMS analysis sequencing. This procedure led us to the identification of 600 phagosomal proteins from murine DC phagosomes. An integrated software solution has been developed to analyse these results and to perform comparative analy...

RDFScape is a plugin that has been developed to extend a software oriented to biological analysis with support for reasoning on ontologies in the semantic web framework. We show with this plugin how the use of ontological knowledge in biological analysis can be extended through the use of inference. In particular, we present two examples relative to ontologies representing biological pathways: we demonstrate how these can be abstracted and visualized as interaction networks, and how reasoning on causal dependencies within elements of pathways can be implemented. A co...

Pathway Processor is a tool for integrating whole-genome expression results into metabolic networks.

Our lab has know-how in the functional annotation of upregulated and downregulated genes by gene ontology classification and pathway analysis by several bioinformatics approaches, among them Ontologizer. Preliminary results obtained from querying DAVID (http://david.abcc.ncifcrf.gov/) and Ontologizer (http://www.charite.de/ch/medgen/ontologizer/) show statistically significant enrichment for immunological-relevant signaling pathways and immunology-related GO terms of the upregulated proteins in mature DCs.

This tool is available through the DC-THERA Directory (see "Pathway Signature Repository "). The procedure allows a user to compare his/her microarray data to the corpus of public immunology experiments stored in DC-BASE using pathway signatures. The procedure is made up by several steps. 1.Raw data normalization: the user uploads raw data (Affymetrix or Illumina gene expression platforms are supported) and select the species. Upon succesful upload, raw data is normalized using a standard procedure. 2.Comparison selection: The user is then asked to select which sa...

The MaxQuant software is designed to make it possible to compare cell subsets quantitatively based on the extracted ion current (XIC) and without any need of stable isotope labels.

We have developed a MAGE-ML export feature in collaboration with the European Bioinformatics Institute (EBI).

The GenePix 4000 software package was used to quantify microarray fluorescence in a yeast microarray experiment.

"The ArrayExpress Tab2MAGE package consists of a set of scripts and modules which can read in microarray experiment annotation in defined spreadsheet formats, combine it with a set of experiment data files, and output the result in MAGE-ML format. Tools are included for validation of these spreadsheet documents, and automation of the entire process. This package can handle two distinct spreadsheet formats: MAGE-TAB, the new community-designed spreadsheet format for microarray data representation and interchange, and the eponymous Tab2MAGE, an older, simpler format u...

Eu.Gene Analyzer is an easy-to-use, stand-alone application that allows rapid and powerful microarray data analysis in the context of biological pathways. Its intuitive graphical user interface makes it an easy and flexible tool, even for the first-time user. Eu.Gene supports a variety of array platforms, organisms and pathway ontologies, transparently deals with multiple nomenclature systems and seamlessly integrates data from different sources. Two different statistical methods, the Fisher Exact Test and the Gene Set Enrichment Analysis (GSEA), are implemented to ide...

DC-STUDIO is a bioinformatics environment enabling the interrogation of DC genomics experiments according to a pathway-based logic. It is integrated with DC-BASE.

In the DC-THERA effort to create new dendritic cell-based therapies, a wide range of information arising from genomics, proteomics, molecular cell biology and pre-clinical models is gathered and applied to the conduction of clinical trials. The DC-THERA Directory is intended to collect and semantically organize this data and to serve as a tool for collaboration among researchers and as a reference point for the information contained. As such it is a directory that provides summarized information and relations between resources and people involved. In particular, we ...

DC-PathEdit is a software based on PathVisio (http://www.pathvisio.org) created for the graphical representation of the pathways and for the establishment of annotations and other properties. It is used as an intermediate step towards the creation of a complete data model of the DC-ATLAS pathways, as it can represent them graphically and also annotate them using a controlled vocabulary.

We have experience in querying DAVID, the Database for Annotation, Visualization and Integrated Discovery (http://david.abcc.ncifcrf.gov/) . For instance, we used DAVID for functional annotation of upregulated and downregulated genes by gene ontology classification and pathway analysis by several bioinformatics approaches. Preliminary results obtained from querying DAVID and Ontologizer (http://www.charite.de/ch/medgen/ontologizer/) show statistically significant enrichment for immunological-relevant signaling pathways and immunology-related GO terms of the upregula...

We have developed an automated microarray data analysis (AMDA) software, which provides scientists with an easy and integrated system for the analysis of Affymetrix microarray experiments. AMDA is free and it is available as an R package. It is based on the Bioconductor project that provides a number of powerful bioinformatics and microarray analysis tools. This automated pipeline integrates different functions available in the R and Bioconductor projects with newly developed functions. AMDA covers all of the steps, performing a full data analysis, including image anal...