Overview of Help-Pages

Genomatix Pathway System (GePS) release notes

September 2011: GePS Release 2.2

• New shape for RNAs with gene IDs
• Network extension for a single gene with all input genes

April 2011: GePS Release 2.1

• Import of additional user data (displayed as circular bullets)
  • Import of metadata for genes from a tab-separated file
  • multiple data-points, can be browsed with the slider like expression data
  • allows to import user data such as
    • Methylation data
    • Phosphorylation data
    • ChIP-Seq data

December 2010: GePS Release 2.0

• Networks can now be created and filtered from
  • all GeneRanker results (like signal transduction pathway or Gene Ontology annotation)
  • all input genes
  • up/down-regulated input genes
  • input genes filtered by literature free text searches
• All filters can be combined with "and" or "or".
• Network extension is possible for all genes in a network/pathway by
  • genes with frequent co-citations
  • transcription factors with frequent co-citations
  • transcriptional downstream targets with frequent co-citations
• Four different co-citations levels are supported (abstract level, sentence level, function word level, and expert level).
• User-defined coloring e.g. for over- and under-expressed genes.
• The network builder allows creating networks from
  • user-defined elements (genes, complexes, DNA, etc.)
  • user-defined interactions / literature-based interactions

August 2010: GePS Release 1.3

• The pathway extension can be customized by different parameters.
  • Minimum number of co-citations
  • Number of genes to be added
  • Maximum number of interactions
  • Connectivity for added genes
  • Restriction on expert curated interactions
• The protein functions are indicated by different node shapes.
  • New shapes: kinase, phosphatase, receptor, transporter, co-factor
• The "cell layout" has been further improved.

March 2010: GePS Release 1.2

• Additional "Export/import" options
  • Pathways can be saved in GePS format.
  • Pathways in GePS format can be re-imported to GePS.
  • "Export gene list" improved, export of selected genes is allowed.
  Note: Export and import of pathways in GePS format requires Adobe Flash Player version 10.
• The "cell layout" has been improved and is now used as default graph layout (instead of "hierarchical layout").
• Modifications in pathway display
  • The number of chemicals that are associated with a gene product is displayed inside the gene product node (in the upper right corner).
  • The total number of interactions of a gene product is displayed in the lower right corner.
  • Biological processes that are affected by the current pathway are drawn as rectangle (like pathways that are affected by the current pathway).

December 2009: GePS Release 1.0

• First release of the Genomatix Pathway System

  The Genomatix Pathway System (GePS) uses information extracted from public and proprietary databases to display more than 400 signal transduction pathways, all manually revised. The diagrams can optionally be overlayed with user data such as gene expression values.

  Please see the help page for an introduction and detailed information.