BiblioSphere
Facts and Figures
Dynamic data-driven network construction based on literature and sequence analysis. The user retains complete control over the analysis process.
BiblioSphere PathwayEdition is the only application which 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 analysed. The integration of sequence analysis applies Genomatix' unique proprietary genome annotation, our proprietary databases for transcription factor binding sites, and the full power of our unique analysis tools.
BiblioSphere PathwayEdition offers three different ways to visualise and analyse gene relations:
- 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
- Cellular component view: Shows the relation in a 2-D network with every gene graphically assigned to a cellular component
- 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
BiblioSphere PathwayEdition is the only application which introduces and superimposes multiple lines of evidence:
- Literature based relations
- Regulatory sequence analysis based relations
- Expert curated gene-transcription factor relations
- Pathway based relations
Evidences for a link between genes are marked by symbols and colors
BiblioSphere PathwayEdition offers different ways of filtering gene relations to only view the most relevant genes:
- Free text filter: Allows you to restrict the network to genes which are cited in literature together with a user defined term
- Co-citation filter: Allows you to restrict the network according to:
- syntactic rules of co-citations
- number of co-citations
- grade of interconnection between genes
- Biological filter: Allows you to restrict the network to genes which are assigned to the same biological class. Classes are defined by:
- Gene Ontology
- Molecular function
- Biological function
- Cellular component
- MESH Terms
- Chemicals and drugs
- Anatomy
- Disease
- Biological sciences
- Analytical, Diagnostic and Therapeutic Techniques and Equipment
- Tissues
- Unique Filter for gene regulators (input genes + transcription factors) automatically verified on sequence level
- Gene Ontology
BiblioSphere PathwayEdition provides statistical analysis of every visible network towards overrepresented and underrepresented gene classes. Statistical analysis is calculated by z-scoring.
BiblioSphere PathwayEdition 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 PathwayEdition is dynamic and purely data driven.
Other systems calculate a priori networks with max. 35 nodes, leaving you in the dark on how those networks were derived.
Genomatix Knowledge Base content
- 105,457 gene IDs for human, mouse, rat, chicken, chimpanzee, zebrafish, rhesus monkey and dog
- 265,036 gene synonyms
- 6,097 gene IDs assigned as transcription factors
- > 300 expert curated function words
- Data mining within > 17 Mio. PubMed abstracts: 42,369,222 gene synonyms were annotated
- Purging of ambiguous gene synonyms and resolution of homonyms:
- 5,484,766 ambiguous gene synonyms were filtered out
- expert supervised semantic resolution of 294,276 homonyms
- 1,638,481 gene-gene interactions (abstract level, sum of all organisms)
- 370,369 gene-transcription factor (TF) interactions (abstract level)
- 989,993 gene-gene interactions (sentence level, sum of all organisms)
- 221,832 gene-TF interactions (sentence level)
- 69,318 gene-gene interactions curated and validated by Genomatix experts
- 56,119 gene-gene interactions curated and validated by Molecular Connections' experts (NetPro database)
Genomatix Knowledge Base structure
Complex Genomatix Knowledge Base Ontology, multi level Taxonomies and Thesauri allow for dynamic superimposition of:
Analysis
- Single gene
- Gene data set from:
- Expression microarray ( differential expression,dose response, time course,...)
- Protein microarray
- Gel electrophoresis
- Protein mass spectrometry
BiblioSphere PathwayEdition calculates complete networks and validates and ranks pathway interactions by z-scoring on basis of Genomatix Knowledge Base Ontology:
- Color coding of nodes according to expression rations or any other numerical attribute in input file
- User focuses network on specific biological/experimental context
- Unsupervised, purely data driven by "following the green path" via z-scoring
- Supervised, by filter settings according to specific area of interest
- Dynamic shortest path calculation and display by double clicking of central gene of interest
- 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
- Superimposition of additional evidence based on promoter sequence analysis
- Superimposition of additional evidence based on expert curated transcriptional regulation knowledge