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This study aimed to deconvolve the levels of infiltrating immune cells in non-small cell lung cancer (NSCLC) and to identify specific gene co-expression modules associated with prognosis of NSCLC. CIBERSORT algorithm was employed to infer the relative abundance of 22 immune cell subtypes in 1751 NSCLC subjects. The patterns of immune infiltration were identified for NSCLC with different clinical and genomic features and were used to construct an immunoscore by LASSO regression associated with NSCLC survival. Weighted gene co-expression n