@tonygill3 If we are specifically interested in pathways, we will move to a linear modelling approach where genes are nested within pathway to allow for a specific test on the pathway. Have to test the co-regulation assumption https://t.co/my2Tl7eZJa
@arbona_vicent @wayneriekhof We actually use neither when we can and go straight to including the pathway structure into our linear model. Came about when we realized a number of pathways had an internal anti-correlation structure https://t.co/wZoPSyyZQH
@pvtodorov @PatrickDeelen @sbmontgom These are the early forms using classical QTL but they also work for GWA as they are simply a way of creating a single phenotype describing a pathway. Time series from a single time point - https://t.co/I29bdYg90O Meta
@BeEngelhardt @emjosephs If you randomize the experiment with replication, then trans are easy to find. https://t.co/S51AuGFtUU Or map using network measures of expression, hides cis. https://t.co/wZoPSyhos7 Do we need a "new" omnigenic model to say tha