SNP to rsID to Overrepresentation

Workflow for mapping SNPs to rsID to performing overrepresentation analysis

flowchart TD

A[SNP file] --> B[[R Shiny]]
Z[rsID list] --> B
B --> C[(AnnoQ)]

C --> |rsIDs| G{{PEREGRINE}}
C --> |rsIDs| D{{ANNOVAR}}
C --> |rsIDs| E{{SnpEff}}
C --> |rsIDs| F{{VEP}}

D --> J1[Ensembl]
D --> J2[RefSeq]

E --> J1
E --> J2

F --> J1
F --> J2

J1 --> |Gene IDs| K[[R Shiny]]
J2 --> |Gene IDs| K
G --> |Gene IDs| K

K --> |unique gene IDs| L[(Panther)]
L --> |Fisher's exact| M[Overrepresentation]

click C "http://annoq.org/" _blank
click L "http://pantherdb.org/" _blank

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The pipeline allows for the user to start from a list of SNPs (Version Seq37) or from a list of rsID.

If you start from the list of SNPs, please refer to SNPs_Seq37_example.csv to see the input format that the R program accepts (this can be modified by the user). Next, you will receive a list of rsID from the R program.

The rsID list will need to be run through ANNOQ to obtain the geneIDs for the SNPs.

Using the Python script you will be able to obtain the unique list of gene IDs, which you will run through Panther.

Overrepresentation Test with Panther

The detailed instruction to run the PANTHER overrespresentation test can be found in the Nature Protocol paper. Briefly,

1. Go to the PANTHER home page: https://pantherdb.org/
2. Click the “Browse” button, and select the unique gene ID list created above.
3. In the Select List Type section, select ID List.
4. In the Select organism section, select Homo sapiens.
5. In the Select Analysis section, select “Statistical overrepresentation test”, then select an annotation data set from the dropdown menu.
6. Click “submit” button.
7. On the next page, in the Default whole-genome lists dropdown menu, select Homo sapien.
8. The page will refresh. Click the Launch analysis button.

Panther will perform a Fisher's exact test to find any overrepresentation in your input list.