Intron Retention Visualization For Important Gene Along PC1

-- T Cell Global Intron Retention Describes patient subtypes in Systemic lupus erythematosus

Background Information

SLE and control samples are able to separate along PC1 direction which matches the overall frequency density distribution using intron retention index. Here we provide IGV visualization for weighted genes from both positive and negative side in PC1 as supplemetary information to the paper.

Systemic lupus erythematosus (SLE) is a complex, multisystem autoimmune disease that involved many vital organs and tissues and predominantly affect women. The clinical symptoms of SLE are highly heterogeneous ranging from mild manifestations in skin and joints inflammation to life-threating condition. While SLE is heritable and genetic factors confer a predisposition to the development of SLE, pure genetic determinants of SLE severity are elusive because of their genetic heterogeneity. Given the autoimmune nature of SLE and the newly-recognized role of intron retention (IR) in global gene regulation for immune cells such as T cells, we studied the global gene expression and intron retention pattern of T cells in SLE patients. The consistency of sample clustering between whole gene expression, spliceosomal protein gene expression and IR pattern indicates an intrinsic correlation that can be used for dimension reduction for gene expression. Moreover, the first principal component of global IR pattern separates SLE into two distinct types and serves as a low-dimension metric to evaluate and diagnose SLE patients.