IPA-Pre-Analysis Filtering (Contextual Data Analy...

Pre-analysis Filtering    (Contextual Data Analysis)

Before running an analysis, species, tissue, disease, fluid, and data source filters can be defined.  As the analysis is run, these filters will be applied to the generation of networks.  For example, if a Mouse-Stringent filter is chosen, then all networks in the resulting analysis will contain only orthologs that include Mouse and all relationships will involve Mouse molecules.

 

These filters are applied to the molecules and the reference set before calculating p-values for functions, canonical pathways, and Tox lists.  For pathways and lists, the filters are applied only to molecules, not relationships.

 

Filter	Effect
Species – Molecules	Consider only orthologs that include members of the selected species
Species – Relationships	Consider only relationships observed in the selected species
Tissue/Cell Line – Orthologs	Consider only orthologs for which (mouse) mRNA is expressed in the selected tissues or cell lines
Tissue/Cell Line -- Relationships	Consider only relationships observed in the selected tissues or cell lines
Data Sources	Consider only relationships obtained from the selected data sources (e.g. Ingenuity or external databases)

 

 

Species Filter

 

 

As a default, all species available are selected for analysis, indicating that IPA does not automatically limit the analysis.

 

The Stringent filter is a highly constrained filter that will return only those molecules and relationships that are very relevant to the selected species; however, because the filter is highly constrained, it may not return many results.  To be specific, the Stringent filter will match molecules that contain an ortholog matching the selected species.  In addition, relationships must involve two molecules that match the selected species, and the location of the relationship must be in the selected species.

 

In contrast, the Relaxed filter is less constrained.  Therefore, the molecules and relationships that it matches may be less targeted, but there may be more results.  To be specific, the Relaxed filter will match molecules that contain an ortholog that includes the selected species.  It filters on the orthologs, but not the relationships between the orthologs.

 

Tissues and Cell Lines Filter

 

 

The Tissues & Cell Lines tab contains a set of tissues and cell lines from which to choose plus two filtering choices: Stringent and Relaxed. As a default, all tissues and cell lines are selected for analysis, indicating that IPA does not automatically limit the analysis.

 

The Stringent filter is a highly constrained filter that will return only those molecules and relationships that are expressed in the selected tissues or cell ines. Since the filter is highly constrained, it may not return many results.

 

In contrast, the Relaxed filter is less constrained.  Therefore, the molecules and relationships that it matches may be less targeted, but there may be more results.  To be specific, the Relaxed filter will match only molecules that are expressed in the selected tissues or cell lines.

 

Data Sources Filter    

 

 

 

The data source filter allows you to choose which data sources you would like to include for your analysis. As a default, all data sources are selected, indicating that IPA does not automatically limit the analysis to a specific data source.

 

Please see click here to see a complete list and detailed explanation of the Data Sources available within IPA.