Objective · To explore the potential mechanisms of gastric cancer (GC), long noncoding RNA (lncRNA) and mRNA profiling of 3 paired GC fresh tissues and their matched adjacent non-cancerous tissues was detected through microarray analysis. Methods · The functions of differentially expressed lncRNA and mRNA were recognizedgene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The co- network was constructed to find the relevance with corresponding mRNAusing hypergeometric cumulative distribution function of MATLAB 2012b and Cytoscape software. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to detect the of 5 differentially expressed key lncRNAs, which were selected in 30 paired GC fresh tissues. Results · Compared with normal tissues, 1 499 lncRNAs and 6 002 mRNAs were dysregulated in GC tissues. The qRT-PCR results showed that the 5 key lncRNAs were consistent with those the microarray data. Cis-regulatory gene analyses showed the chromosome location of these key lncRNAs, and revealed the associated co-expressed genes. The trans-analyses results demonstrated that enormous transcription factors regulated lncRNA and gene . Conclusion · These differentially expressed lncRNAs in GC may be promising biomarkers and provide valuable information for GC targeted treatment.