Table 4. Top 10 pathways identified by MAGMA (standalone) gene-set analysis (including genome-wide SNPs) using duration as phenotype.

Category	Pathway	NGENES	BETA	Pvalue	Bonf. Corr. Pvalue
Gene ontology	regulation of calcium ion import across plasma membrane	2	2.86	2.57 x 10−6	0.04
Gene ontology	regulation of T-lymphocyte activation via T cell receptor contact with MHC-bound antigen	5	1.58	5.41 x 10−6	0.09
Gene ontology	cellular response to copper	11	1.04	2.55 x 10−5	0.43
Gene ontology	proteosomal ubiquitin-independent protein catabolic process	4	1.51	6.25 x 10−5	1.00
Gene ontology	anchored component of external side of plasma membrane	18	0.77	1.06 x 10−4	1
Gene ontology	response to iron ion	30	0.61	1.11 x 10−4	1
Gene ontology	obsolete intrinsic component of external side of plasma membrane	23	0.69	1.16 x 10−4	1
Gene ontology	T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	8	1.06	1.27 x 10−4	1
Gene ontology	CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation	4	1.33	3.44 x 10−4	1
Gene ontology	positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	2	1.67	3.52 x 10−4	1

(NGENES = number of genes in the gene-set dataset; BETA = regression coefficient of the gene set)