BackgroundColorectal cancer (CRC) was one of the most commonly diagnosed malignancies. The molecular mechanisms involved in the progression of CRC remain unclear. Accumulating evidences showed that long noncoding RNAs (lncRNAs) played key roles in tumorigenesis, cancer progression, and metastasis. Therefore, we aimed to explore the roles of lncRNAs in the progression of CRC.MethodsIn this study, we aimed to identify differentially expressed lncRNAs and messenger RNAs (mRNAs) in CRC by analyzing a cohort of previously published datasets: GSE64857. GO and KEGG pathway analyses were applied to give us insight in the functions of those lncRNAs and mRNAs in CRC.ResultsTotally, 46 lncRNAs were identified as differentially expressed between stage II and stage III CRC for the first time screening by microarray. GO and KEGG pathway analyses showed that differentially expressed lncRNAs were involved in regulating signal transduction, cell adhesion, cell differentiation, focal adhesion, and cell adhesion molecules.ConclusionsWe found three lncRNAs (LOC100129973, PGM5-AS1, and TTTY10) widely co-expressed with differentially expressed mRNAs. We also constructed lncRNA-associated PPI in CRC and found that these lncRNAs may be associated with CRC progression. Moreover, we found that high PGM5-AS1 expression levels were associated with worse overall survival in CRC cancer. We believe that this study would provide novel potential therapeutic and prognostic targets for CRC.Electronic supplementary materialThe online version of this article (doi:10.1186/s12957-017-1211-7) contains supplementary material, which is available to authorized users.

The objective of this study was to investigate the key genes and pathways associated with thyroid carcinoma. Based on the microarray data of GSE27155, we identified the differentially expressed genes (DEGs) between four types of thyroid carcinoma samples (papillary carcinoma (PTC), oncocytic carcinoma (OTC), follicular carcinoma (FTC) and anaplastic carcinoma (ATC)) and normal controls. With the obtained DEGs, we performed gene functional interaction (FI) network analysis. Then we conducted Venn diagram analysis to identify the intersection and specific DEGs of the four types of thyroid carcinomas. The intersections DEGs were performed by functional enrichment and transcription factor (TF) prediction analyses. These specific DEGs were performed by pathway enrichment analysis. There were respectively 323, 318, 118 and 1005 DEGs identified in PTC, OTC, FTC and ATC. Twelve sub-network modules were extracted based on gene FI network analysis and eight thyroid carcinoma-associated DEGs were involved in the network, such as TIMP1. Based on the Venn diagram analysis, 27 common DEGs were identified, such as HMGB3 which was regulated by TF of NKX3-1. There were 149 PTC-specific DEGs (like CLDN1), 160 OTC-specific DEGs, 94 FTC-specific DEGs (like PPARG), and 789 ATC-specific DEGs (like CDK1). They were enriched in some pathways, such as Cell cycle, Citrate cycle, and Oxidative phosphorylation. TIMP1, HMGB3, CLDN1, CDK1 and PPARG as well as pathways of Cell cycle, Citrate cycle, and Oxidative phosphorylation may play important roles in the progression of thyroid carcinoma.