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Category Cross-Omics>Pathway Analysis/Tools Abstract BiblioSphere Pathway Edition is an advanced pathway analysis system. It uses one of the world's largest databases of biological networks created from millions of individually modeled relationships between genes, proteins, complexes, cells and tissues. A unique combination of hand curation from biological experts and up- to-date text mining techniques for automated knowledge extraction provides you with some of the best data quality available. BiblioSphere PathwayEdition allows a view on your data, integrated in biological networks according to different biological context. This unique feature results from multiple 'lines of evidence' which are integrated in BiblioSphere PathwayEdition's database. Additional product features/capabilities include: Product automatically creates the entire network of input genes, correlated genes and their biological connections. Its various tools offer support to facilitate focusing on the biological context most relevant for your research. There is No upper limit for networks to be analyzed. The integration of sequence analysis applies Genomatix' unique proprietary genome annotation, Genomatix' proprietary databases for transcription factor binding sites, and the full power of Genomatix' unique analysis tools. BiblioSphere Pathway Edition offers three (3) different ways to visualize and analyze gene relations - 1) Network view - Shows the relations in a 2-D network. By double clicking on a node the network dynamically shifts the focus to that gene, showing the shortest path between your gene of interest and the genes in the network; 2) Cellular component view - Shows the relation in a 2-D network with every gene graphically assigned to a cellular component; 3) 3-D view - Shows genes in a real time interactive 3-D sphere which represents the strength of relationship between genes by the distance between the elements. Product introduces and superimposes 'multiple lines of evidence' via - 1) Literature based relations; 2) Regulatory sequence analysis based relations; 3) Expert curated gene-transcription factor relations; 4) Pathway based relations. Evidences for a link between genes are marked by symbols and colors. BiblioSphere Pathway Edition offers different ways of filtering gene relations to only view the most relevant genes - 1) Free text filter - Allows you to restrict the network to genes which are cited in literature together with a user defined term; 2) Co-citation filter - Allows you to restrict the network according to - a) syntactic rules of co-citations, b) number of co-citations, c) grade of inter-connection between genes; 3) Biological filter - Allows you to restrict the network to genes which are assigned to the same biological class. Classes are defined by - a) Gene Ontology (GO) - Molecular function, Biological function and Cellular component; b) MESH Terms - Chemicals and drugs, Anatomy, Disease, Biological sciences, Analytical, Diagnostic and Therapeutic Techniques and Equipment; c) Tissues; d) Unique Filter for gene regulators (input genes + transcription factors) automatically verified on sequence level. Product provides statistical analysis of every visible network towards overrepresented and underrepresented gene classes. Statistical analysis is calculated by z-scoring. BiblioSphere Pathway Edition offers integrated functionality of statistical analysis and filtering - A single click filters a network to those genes which are overrepresented according to GO or MESH class. The network/pathway construction of BiblioSphere Pathway Edition is dynamic and purely data driven. Genomatix Knowledge Base structure - Complex Genomatix Knowledge Base Ontology, multi level Taxonomies and Thesauri allow for dynamic superimposition of - 1) 20 different filters (including free text filter in 11 classes); 2) MESH: > 3.11 million MESH annotations of 17,000 MESH terms in 5 main categories; 3) GO: > 150,000 annotations of 10,771 terms in 3 main categories; 4) Tissue: > 2.27 million annotations to 459 tissue types of Genomatix proprietary hierarchical tissue atlas plus 244 UniGene tissues. Analysis features - Input - 1) Single gene or 2) Gene data set from - a) Expression microarray (differential expression, dose response, time course,...); b) Protein microarray; c) Gel electrophoresis; d) Protein mass spectrometry. BiblioSphere Pathway Edition calculates complete networks and validates and ranks pathway interactions by z-scoring on basis of Genomatix Knowledge Base Ontology. 1) Color coding of nodes according to expression rations or any other numerical attribute in input file; 2) User focuses network on specific biological/experimental context - a) Unsupervised, purely data driven by "following the green path" via z-scoring, b) Supervised, by filter settings according to specific area of interest; 3) Dynamic shortest path calculation and display by double clicking your central gene of interest; 4) Automatic integration of pathway/network relevant transcription factors, even if those are Not elements of the input set. Optional expansion by all other genes in the network beyond input list and transcription factors; 5) Superimposition of additional evidence based on promoter sequence analysis; 6) Superimposition of additional evidence based on expert curated transcriptional regulation knowledge. System Requirements One of the following operating systems: Windows 9x, 2000, XP (Please contact support@genomatix.de for installation on XP 64bit! Linux/Unix, MacOS X (at least 10.4) Java 1.5.0_06 or higher. Internet connection 512 MB main memory
Bayerstr. 85a 80335 München Germany Phone: +49-89-599-766-0 Fax: +49-89-599-766-55 email: info@genomatix.de sales: sales@genomatix.de Genomatix Software Inc. 2900 Huron Parkway, Suite 100 Ann Arbor, MI 48104 USA Phone: +1-877-436-6628, +1-877-GENOMAT Fax: +1-734-622-0477 email: sales@genomatix-software.com Manufacturer's Web Site www.genomatix. de/products/BiblioSphere/BiblioSpherePE1.html Price Contact manufacturer G6G Product Number 20019 G6G Manufacturer Number 101114 |
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