Datapunk Opus 23 Pro

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GWASFED: Genome Wide Association Study data in detail

The GWASFED app allows you to perform a traditional search of PubMed. Depending on the article, it may supply you with additional information from the Opus 23 Pro databases.

Getting around GWASFED

From the 'Informatics' link on the main menu, hover over 'Analytics' until a second menu list appears, then select GWASFED.

GWASFED data screen. Like most data-driven apps in Opus 23 Pro, GWASFED uses a filterable/sortable table to display its data. At the bottom of the window is a jump table that allows you to move from one screen to the next. You can control how many rows to display by selecting an option from the 'Show' pull down menu. The default is 15.

Filtering and sorting results

As you can see there are over 100+ pages of etiology data in GWASFED, making grinding through the data impractical. To deal with large amounts of data, GWASFED features a 'filterable' display. Type full or partial search terms into the search box at the upper left hand corner and GWASFED immediately displays only those results. Click on any column title to sort by that column. Click that column again to reverse the sort order. Click on the NOTEPAD icon to add or edit a note for that disease / trait.

The default sort in GWASFED is by 'Wow Factor', a semi-synthetic number that is calculated by the aggregate log p-value and the distribution and effects of the related SNPs and their power factor. Click on the disease/ trait to bring up a pop-up window with the PubMed citation.

Each row in GWASFED depicts the following:

Disease/ trait
Aggregate log p value
Wow Factor
Number of disease SNPs
Client SNPs and Heterozygous and Homozygous count
Risk Allele Frequency and Effects

The 'Risk Allele Frequency and Effects' affords considerable insight into the nature of the client’s relationship with the disease/ trait. Rare or low frequency SNPs with large effects will probably be more noteworthy than small effect SNPs with large frequencies.