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      • Record: found
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      Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares

      research-article
      Author(s): 1 , 2 , 3 , 1 , 4 , 1 , 1 ,
      Publication date (Electronic):
      Journal: BMC Proceedings
      Publisher: BioMed Central
      Conference name: EADGENE and SABRE Post-analyses Workshop
      Conference date: 12–14 November 2008

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          Abstract

          Background

          As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these results.

          Results

          GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes. The three softwares allowed the analysis of the data and highlighted different networks. However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation.

          Conclusion

          Combining these databases that were developed independently on different annotation sources supplies a useful tool for a global biological interpretation of microarray data, even if they may contain some imperfections (e.g. gene not or not well annotated).

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
          Article 0 comments Cited 15331 times – based on 0 reviews     Review now
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            GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

            Bing Zhang, Denise Schmoyer, Stefan Kirov … (2004)
            Background Microarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in the gene sets. Results We have created a web-based tool for data analysis and data visualization for sets of genes called GOTree Machine (GOTM). This tool was originally intended to analyze sets of co-regulated genes identified from microarray analysis but is adaptable for use with other gene sets from other high-throughput analyses. GOTree Machine generates a GOTree, a tree-like structure to navigate the Gene Ontology Directed Acyclic Graph for input gene sets. This system provides user friendly data navigation and visualization. Statistical analysis helps users to identify the most important Gene Ontology categories for the input gene sets and suggests biological areas that warrant further study. GOTree Machine is available online at . Conclusion GOTree Machine has a broad application in functional genomic, proteomic and other high-throughput methods that generate large sets of interesting genes; its primary purpose is to help users sort for interesting patterns in gene sets.
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              Comparison of transcriptional changes associated with E. acervulina and E. maxima infections using cDNA microarray technology.

              C KEELER, Charles C. Hong, H Lillehoj … (2007)
              Enhanced understanding of host-pathogen interactions at local sites of infection will extend our knowledge of disease pathogenesis and will facilitate the development of novel preventive methodologies against many infectious diseases of economic importance. In the current study, a 9.6K avian intestinal intraepithelial lymphocyte cDNA microarray (AVIELA) was developed to compare the local transcriptional profiles following primary and secondary infections with two major Eimeria parasites, E. acervulina (EA) and E. maxima (EM), which infect the intestinal duodenum and jejunum, respectively. Gene Ontology analyses showed that EAinfection primarily induced genes associated with lipid metabolism and intracellulartrafficking whereas EM infection upregulated the genes involved in protein biosynthesis and metabolism, and downregulated apoptosis related genes. Following primary EA infection, there was a significantly enhanced expression of genes involved in the signal pathway of T cell activation and cytoskeletal regulation. Thus, the AVIELA array provides a valuable tool for investigating host-pathogen interactions in avian coccidiosis and allows for the comparison of the transcriptional regulations induced by species of Eimeria that infect different areas of the intestine.
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                Author and article information

                Conference
                Journal ID (nlm-ta): BMC Proc
                Title: BMC Proceedings
                Publisher: BioMed Central
                ISSN (Electronic): 1753-6561
                Publication date Collection: 2009
                Publication date (Electronic): 16 July 2009
                Volume: 3
                Issue: Suppl 4
                Page: S11
                Affiliations
                [1 ]INRA, UMR444, Laboratoire de Génétique Cellulaire, F-31326 Castanet-Tolosan, France
                [2 ]INRA, UMR 598, Génétique Animale, F-35000 Rennes, France
                [3 ]Agrocampus Ouest, UMR 598 Génétique Animale, F-35000 Rennes, France
                [4 ]INRA, UR631, Station d'Amélioration Génétique des Animaux, F-31326 Castanet-Tolosan, France
                Article
                Publisher ID: 1753-6561-3-S4-S11
                DOI: 10.1186/1753-6561-3-S4-S11
                PMC ID: 2712741
                PubMed ID: 19615111
                SO-VID: 0ae1ae6a-d512-4191-a4f5-bda8876cc1b4
                Copyright © Copyright © 2009 Bonnet et al; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Conference name: EADGENE and SABRE Post-analyses Workshop
                Conference location: Lelystad, The Netherlands
                Conference date: 12–14 November 2008
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                Subject: Research

                ScienceOpen disciplines: Medicine
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                ScienceOpen disciplines: Medicine

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