Reviewing Mapped Identifiers

Reviewing Mapped Identifiers

The following lists are generated after identifier mapping is complete.

Mapped IDs are identifiers that were successfully mapped to a molecule in the Ingenuity Knowledge Base.  Duplicate identifiers are mapped to a single molecule. Mapping of external identifiers to molecules in the Ingenuity Knowledge Base is performed using information in Homologene.

Unmapped IDs are identifiers that were not mapped to a molecule in the Ingenuity Knowledge Base. Unmapped molecules may fall into one of the following categories:

1) The gene/protein ID does not correspond to a known gene product.  For example, most ESTs are not found in the Ingenuity Knowledge Base (exception: ESTs that have a corresponding Entrez Gene identifier are in the Ingenuity Knowledge Base).

2) The identifier is associated with more than one Entrez Gene ID and is therefore left unmapped in the application due to the ambiguity of its identity.  Some possible causes are:

• Conflicting annotations that map to multiple genes (for example, an identifier is associated with two refseq ids that map to different genes)

• dbSNP identifiers that lie within the flanking regions of multiple genes

• Older Illumina probe identifiers (IDs) that have an integer format (e.g. 12345).  More current Illumina probe IDs start with GI or IL, for example GI_12345678 and IL_12345.  The older Illumina integer IDs overlap between species of Illumina expression arrays so IPA cannot guarantee mapping to the correct gene.  Users should instead use Refseq IDs.

3) The identifier format may be shared by multiple sources (for example, Entrez Gene and PubChem both use integer values).  IPA attempts a “best guess” based on mapping percentages, but please check the Source Type to make sure the correct one(s) are selected.

If you have an identifier that is not being mapped in IPA and you think it should be, please contact Customer Support at 650-381-5111 or Support@ingenuity.com. We can research why individual identifiers are not mapped. Please tell us the identifier in question, the identifier type you are using, the molecule you think it should map to, and the molecule that it is mapping to in IPA (if you think it is a mismapping).

All IDs are all of the identifiers contained in the dataset file.

Network Eligible Molecules are the molecules that are eligible for network generation.  In order for a molecule to become a Network Focus molecule, it must meet two criteria.

1) It must meet all of the criteria you specified in your analysis parameters. (i.e. Must meet the cutoff value, focus on, and directionality.)

2) There must be at least one other molecule in the Ingenuity Knowledge Base that interacts with it.

Functions/Pathways Molecules are the molecules eligible for functional analysis. In order for a molecule to become a Functions/ Pathway Molecule, it must meet two criteria.

1) It must meet all of the criteria you specified in your analysis parameters. (i.e. Must meet the cutoff value, focus on, and directionality.)

2) There must be at least one functional annotation (function, pathway or list)  associated with this molecule in the Ingenuity Knowledge Base.

NOTES:

1) A molecule can be both a Network Eligible molecule and a Functions/ Pathway Eligible molecule if it meets all 3 criteria specified above.

2) You can change the number of Network Molecules or Functions/ Pathways Eligible Molecules by changing the analysis parameters.

To review the mapped genes in your dataset follow the steps below.

Before an analysis has been run

Scroll down to the bottom of the Create Analysis window to see the Dataset File Mapping.

After an analysis has been run

1) The button can be used throughout IPA to view your analysis settings. This button is available from the following pages:

List of Networks

Functions (Global)

Canonical Pathways (Global)

My Pathways Analysis

Gene Summary

Network Explorer

Overlapping Networks

My Lists

Annotations

or

2) Right click on the Analysis name from the Project Manager and select, Settings