Type I interferons (IFNs) are pleiotropic cytokines that modulate both innate and adaptive immune responses. They have been used to treat autoimmune disorders, cancers, and viral infection and have been demonstrated to elicit differential responses within cells, despite sharing a single receptor. The molecular basis for such differential responses has remained elusive. To identify the mechanisms underlying differential type I IFN signaling, we used whole genome microarrays to measure longitudinal transcriptional events within human CD4 ϩ T cells treated with IFN-␣2b or IFN-1a. We identified differentially regulated genes, analyzed them for the enrichment of known promoter elements and pathways, and constructed a network module based on weighted gene coexpression network analysis (WGCNA). WGCNA uses advanced statistical measures to find interconnected modules of correlated genes. Overall, differential responses to IFN in CD4 ϩ T cells related to three dominant themes: migration, antigen presentation, and the cytotoxic response. For migration, WGCNA identified subtypespecific regulation of pre-mRNA processing factor 4 homolog B and eukaryotic translation initiation factor 4A2, which work at various levels within the cell to affect the expression of the chemokine CCL5. WGCNA also identified sterile ␣-motif domain-containing 9-like (SAMD9L) as critical in subtype-independent effects of IFN treatment. RNA interference of SAMD9L expression enhanced the migratory phenotype of activated T cells treated with IFN- compared with controls. Through the analysis of the dynamic transcriptional events after differential IFN treatment, we were able to identify specific signatures and to uncover novel genes that may underpin the type I IFN response.human; T cell; cytokines; gene regulation INTERFERONS (IFNs) are pleiotropic molecules implicated in a wide range of cellular responses (44) and are Federal Drug Administration-approved therapeutics for the treatment of cancer, infection, and autoimmunity (49). Based on sequence homology and structure, IFNs are divided into three classes: types I, II, and III. Type I IFNs include IFN-␣ (15 known ␣-subtypes), IFN-, and IFN-, whereas type II IFN consists only of IFN-␥ and type III IFN consists only of IFN-. All type I IFNs activate a common cell surface receptor [the IFN receptor (IFNR)], which exists as two separate polypeptides (IFNAR1 and IFNAR2) with no intrinsic dimerization capacity (12). Binding of type I IFNs to IFNAR2, recruitment of IFNAR1, and stabilization of a heterotrimeric ligand/receptor complex activate members of the Jak1/tyrosine kinase 2 (Tyk2) and JAK/STAT pathways (12, 45). Phosphorylated STAT1/ STAT2 heterodimers form transcriptional activation complexes with IFN regulatory factor (IRF)9/p48, translocate to the nucleus, and drive the expression of numerous genes, including myxovirus resistance protein 1 (MX1), 2Ј,5Ј-oligoadenylate synthetase 1, and double-stranded RNA-activated protein kinase (EIF2AK2).Although type I IFNs share the same cognate receptor and und...