Ricardo Martínez, Nicolas Pasquier, C. Pasquier, M. Collard, Lucero Lopez-Perez
{"title":"Co-expressed gene group analysis (CGGA): An automatic tool for the interpretation of microarray experiments","authors":"Ricardo Martínez, Nicolas Pasquier, C. Pasquier, M. Collard, Lucero Lopez-Perez","doi":"10.2390/biecoll-jib-2006-37","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2006-37","url":null,"abstract":"Microarray technology produces vast amounts of data by measuring simultaneously the expression levels of thousands of genes under hundreds of biological conditions. Nowadays, one of the principal challenges in bioinformatics is the interpretation of this large amount of data using different sources of information. We have developed a novel data analysis method named CGGA (Co-expressed Gene Groups Analysis) that automatically finds groups of genes that are functionally enriched, i.e. have the same functional annotations, and are co-expressed. CGGA automatically integrates the information of microarrays, i.e. gene expression profiles, with the functional annotations of the genes obtained by the genome-wide information sources such as Gene Ontology. By applying CGGA to wellknown microarray experiments, we have identified the principal functionally enriched and co-expressed gene groups, and we have shown that this approach enhances and accelerates the interpretation of DNA microarray experiments.1","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123382274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"MILAN - A medical information-system linking agents to metabolic networks","authors":"B. Prins, R. Hofestädt","doi":"10.2390/biecoll-jib-2006-45","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2006-45","url":null,"abstract":"The genome, the protein-biosynthesis and the metabolism constitute a complex, strongly linked system. The complete functionality of this system is not entirely understood yet. Especially pharmacologists and medical doctors are interested to know how the system works regarding the influence of medications (Drug-Pointing). In the last thirty years biochemical research delivered a huge amount of relevant data for this field. The problem is, that all this data is highly distributed in thousands of databases which are just partly interconnected. Gathering and interconnecting this large amount of distributed data by hand significantly slows down the research process. Hence it is vitally important to create tools in terms of information-systems, which support the process of understanding through automatic data-integration and analysis. In this paper we would like to introduce our approach of a corresponding information-system. MILAN is an extensible datawarehouse framework, which has already integrated about 7.7 million medical publication-abstracts as well as metabolic pathways and information about enzymes, ligands, agents and pharmaceuticals from a collection of major biochemical databases. The system provides a set of functionalities to show where the metabolism is affected by a certain drug and instantly displays the most relevant publications for the particular case. Future development will focus on the integration of more databases and the development of additional functions like detection of side-effects and drug-interactions.","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129983054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
E. Souche, B. Hellemans, J. Houdt, A. Canario, S. Klages, R. Reinhardt, F. Volckaert
{"title":"Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags","authors":"E. Souche, B. Hellemans, J. Houdt, A. Canario, S. Klages, R. Reinhardt, F. Volckaert","doi":"10.2390/biecoll-jib-2007-73","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2007-73","url":null,"abstract":"Marine Genomics Europe (MGE) is a European Network of Excellence for the implementation of high-throughput genomic approaches in the biology of marine organisms. Three different genomic aspects are addressed: functional, comparative and environmental genomics. European sea bass (Dicentrarchus labrax) is one of the model organisms studied within MGE. Sequencing of Expressed Sequence Tags (ESTs) from 14 tissue cDNA libraries was carried out to support the different genomic research sections. The EST information can be used to assess various genomic characteristics, such as the discovery of genomic polymorphisms.","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130858717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joel P. Arrais, Bruno Santos, João Fernandes, L. Carreto, Manuel A. S. Santos, J. Oliveira
{"title":"GeneBrowser: an approach for integration and functional classification of genomics data","authors":"Joel P. Arrais, Bruno Santos, João Fernandes, L. Carreto, Manuel A. S. Santos, J. Oliveira","doi":"10.2390/biecoll-jib-2007-82","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2007-82","url":null,"abstract":"The achievements coming from genome analysis depend greatly on the quality of computational and processing methods. Tools for functional mRNA profiling and for gene information integration have become essential to this task. We have developed GeneBrowser as a novel approach that combines the advantages of mRNA profiling tools, at genome-scale experiments, with the features provided by data integration systems. For a given set of genes, GeneBrowser integrates bibliography information with functional annotations, using Gene Ontology, Entrez Gene, KEGG Orthology and KEGG Pathways. The result is a comprehensive and easy to use web application that helps researchers to extract knowledge from large data sets and to speed up the discovery process.","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128771840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sabah Khalid, Mohsin A.F. Khan, Alistair L. J. Symonds, K. Fraser, Ping Wang, Xiaohui Liu, Suling Li
{"title":"CIDA: An integrated software for the design, characterisation and global comparison of microarrays","authors":"Sabah Khalid, Mohsin A.F. Khan, Alistair L. J. Symonds, K. Fraser, Ping Wang, Xiaohui Liu, Suling Li","doi":"10.2390/biecoll-jib-2007-78","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2007-78","url":null,"abstract":"Microarray technology has had a significant impact in the field of systems biology involving the investigation into the biological systems that regulate human life. Identifying genes of significant interest within any given disease on an individual basis is no doubt time consuming and inefficient when considering the complexity of the human genome. Thus, the genetic profiling of the entire human genome in a single experiment has resulted in microarray technology becoming a widely used experimental tool. However, without the use of tools for several aspects of microarray data analysis the technology is limited. To date, no such tool has been developed that allows the integration of numerous microarray results from different research laboratories as well as the design of customised gene chips in a cost-effective manner. In light of this, we have designed the first integrated and automated software called Chip Integration, Design and Annotation (CIDA) for the cross comparison, design and functional annotation of microarray gene chips. The software provides molecular biologists with the control to cross compare the biological signatures generated from multiple microarray studies, design custom microarray gene chips based on their research requirements and lastly characterise microarray data in the context of immunogenomics. Through the relative comparison of related microarray experiments we have identified 258 genes with common gene expression profiles that are not only upregulated in anergic T cells, but also in cells over-expressing the transcription factor Egr2, that has been identified to play a role in T cell anergy. Using the gene chip design aspect of CIDA we have designed and subsequently fabricate immuno-tolerance gene chips consisting of 1758 genes for further research. The software and database schema is freely available at ftp://ftp.brunel.ac.uk/cspgssk/CIDA/. Additional material is available online at http://www.brunel.ac.uk/about/acad/health/healthres/researchgroups/mi/publications/supp lementary/cida","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129941522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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