Improved ease of use and increased search capabilities
The Search tool in IPA is now easier to use because all search options have been consolidated to the main tool bar. Furthermore, you can speed up your research by finding entities (i.e., genes, chemicals, diseases and biological functions) of interest inside Canonical Pathways and Tox Lists. You can also search for your own custom pathways and lists either by name or by entities within them — even in notes you have added to the pathways.
For example, you can search for a gene name, such as “FASLG”, and find all the pathways and lists in which the gene participates (Figure 1).
Figure 1. A search for FASLG in “Pathways and Lists” returned 57 Canonical Pathways and Tox Lists in which FASLG is a participant. In prior releases of IPA, this query would not have returned results, as the prior search tool searched pathway names and categories only, and did not search entities contained within the pathways or lists.
Likewise, a search for a disease of function term will find Canonical Pathways or Tox Lists for which the term is either in a node on the pathway or in the pathway’s name (Figure 2).
Figure 2. Searching for a disease node within pathways and lists finds one match in the name of one pathway and several matches inside another pathway.
For Canonical Pathways, the search automatically “expands” groups and complexes to look within them for genes and protein names. For example, a search for RAF, ARAF, BRAF or RAF1 would return a Canonical Pathway that contains the group “RAF”. Note, however, that, when you open the pathway, you will not immediately see the ARAF, BRAF or RAF1 nodes as they are members of the RAF group, which appears as a single node in the diagram. You can manually expand the RAF node to view these molecules using the “Expand Members/Membership” option available in the Graph Options button in the My Pathways toolbar or from the menu that appears when you right-click the group.
~83,000 Expert findings
~187,000 protein–protein interaction findings from BioGrid
~4,600 gene-to-cancer-type findings from Catalogue of Somatic Mutations in Cancer (COSMIC)
~1,800 target-to-disease findings from ClinicalTrials.gov
~1,800 drug-to-disease findings from ClinicalTrials.gov
~1,000 newly mappable chemicals
~950 gene-to-disease associations from Online Inheritance in Man (OMIM)
~600 protein–protein-interaction findings from IntAct
~300 gene-to-disease or -phenotype associations from the Mouse Genome Database (MGD or "Jax”)
~180 chemical-to-cancer findings from the Chemical Carcinogenesis Research Information System (CCRIS)
~14,000 cancer-mutation findings from ClinVar
~600 target-to-disease findings from ClinicalTrials.gov
~800 drug-to-disease findings from ClinicalTrials.gov
~55 newly mappable chemicals
~1,000,000 RNA expression-to-cell-type findings from The Human Protein Atlas (THPA). In this release, this new content source is used only for filtering in Tissue and Cell Lines filters and includes 49 cell types.