Bioinformatics and systems biology analysis of the gene expression and RNA interaction profiling in the Esophageal cancer-related signaling pathway
Bioinformatics and systems biology analysis of the gene expression and RNA interaction profiling in the Esophageal cancer-related signaling pathway
Marzie Heydari,1Fateme Moradi,2Mohammad Rezaei,3Mansoureh Azadeh,4,*
1. Zist fanavari Novin Biotechnology Institute, Isfahan, Iran 2. Zist fanavari Novin Biotechnology Institute, Isfahan, Iran 3. Zist fanavari Novin Biotechnology Institute, Isfahan, Iran 4. Zist fanavari Novin Biotechnology Institute, Isfahan, Iran
Introduction: Esophageal cancer (EC) is the eleventh most common cause of cancer worldwide and the sixth most common cause of cancer-related mortality [1]. The purpose of this study is to find a novel differentially expressed genes (DEGS) in the EC patients compared to control samples and signaling pathway.
Methods: gene expression data of EC patients (GSE161533) was obtained from the NCBI Gene Expression Omnibus (GEO) and then analyzed by GEO2R to find differentially expressed genes (DEGs) and validation of expression analyses performed by GEPIA2 [2] and ENCORI [3] database. Through GeneCards [4] and Enrichr [5], gene ontology information and biological pathway involvement were understood. Furthermore, miRWalk [6] was utilized to find significant miRNA-mRNA interactions. And the selected miRNA was searched in LncBase V.3 [7] to find strong interactions with LncRNAs and construct a predictive ceRNA network.
Results: Based on microarray analysis, MMP1 have a significant up-regulation in the EC samples, compared to control (|logFC| =6.779 , adj. P value =3.67e-23). This gene encodes a member of the peptidase M10 family of matrix metalloproteinases (MMPs). Proteins in this family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. And the product of this gene is involved in the PPAR signaling pathway. hsa-miR-324-5 (score=1 , energy=-29.2) is a novel suppressor for MMP1. hsa-miR-324-5p have a RNA interactions with SLFNL1-AS1 and LINC00863 LncRNAs.
Conclusion: MMP1 is overexpressed in EC and forms a possible ceRNA network among hsa-miR-324-5p , SLFNL1-AS1 and LINC00863. So we assume that this network can participate in PPAR signaling pathway.