Altered long noncoding RNA (lncRNA) and mRNA is vital in the progression from infection to gastric cancer (GC) and mucosa-associated lymphoid tissue (MALT) lymphoma. Five independent Gene Expression Omnibus datasets (GSE5081, GSE84433, GSE15459, GSE66229 and GSE25638) were included in our study. Differentially expressed lncRNAs and mRNAs in both -positive gastritis and GC tissues were identified. Using two GC cohorts, the -related mRNA and were independent predictors of overall survival. Moreover, the expressions of lncRNA and 44 mRNAs were significantly changed in gastric MALT lymphoma patients. The lncRNA/mRNA response to infection in gastritis and GC influence the outcome of GC and progression of MALT lymphoma.